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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Issue while Installing on Fedora HPC Using conda environment #461

Open Stack7 opened 3 weeks ago

Stack7 commented 3 weeks ago

Hey! I am opening this issue since I have got issues on Installing SCENIC+ on a Fedora HPC, using as higly recommended a conda enviroment.

I have follwed the instruction in the [https://scenicplus.readthedocs.io/en/latest/install.html]:

conda create --name scenicplus python=3.11

conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus
git checkout development
pip install .

and I obtain this:

Error output

Processing /orfeo/cephfs/home/cdslab/astacchetti/scenicplus
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting loomxpy@ git+https://github.com/aertslab/LoomXpy@main (from scenicplus==1.0a1)
  Cloning https://github.com/aertslab/LoomXpy (to revision main) to /tmp/pip-install-qgvhkvqb/loomxpy_85f0cc5b6a3f424ab3cae26c1fc4276e
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/LoomXpy /tmp/pip-install-qgvhkvqb/loomxpy_85f0cc5b6a3f424ab3cae26c1fc4276e
  Resolved https://github.com/aertslab/LoomXpy to commit 61995ff10940968eac2cee8fe48300ab477a15d0
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pycistarget@ git+https://github.com/aertslab/pycistarget (from scenicplus==1.0a1)
  Cloning https://github.com/aertslab/pycistarget to /tmp/pip-install-qgvhkvqb/pycistarget_65183d13b6b444aca75a4b949062f031
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycistarget /tmp/pip-install-qgvhkvqb/pycistarget_65183d13b6b444aca75a4b949062f031
  Resolved https://github.com/aertslab/pycistarget to commit 8cd78f110f4eeeb38d8f7006a1100a13d636d984
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pycistopic@ git+https://github.com/aertslab/pycisTopic (from scenicplus==1.0a1)
  Cloning https://github.com/aertslab/pycisTopic to /tmp/pip-install-qgvhkvqb/pycistopic_577306b40a034eca8f9a21fdb4c0e8aa
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pycisTopic /tmp/pip-install-qgvhkvqb/pycistopic_577306b40a034eca8f9a21fdb4c0e8aa
  Resolved https://github.com/aertslab/pycisTopic to commit bc901b4318562578851c6431891d441fc6779446
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pyscenic@ git+https://github.com/aertslab/pySCENIC@master (from scenicplus==1.0a1)
  Cloning https://github.com/aertslab/pySCENIC (to revision master) to /tmp/pip-install-qgvhkvqb/pyscenic_45cf4b15aeee4f9bb5ca77b5ff9c687e
  Running command git clone --filter=blob:none --quiet https://github.com/aertslab/pySCENIC /tmp/pip-install-qgvhkvqb/pyscenic_45cf4b15aeee4f9bb5ca77b5ff9c687e
  Resolved https://github.com/aertslab/pySCENIC to commit d2309fed83759a0e66e0a995ef3d2f40bf4d6c1a
  Preparing metadata (setup.py) ... done
Collecting adjusttext==1.0.4 (from scenicplus==1.0a1)
  Using cached adjustText-1.0.4-py3-none-any.whl.metadata (3.0 kB)
Collecting aiohttp==3.9.3 (from scenicplus==1.0a1)
  Using cached aiohttp-3.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.4 kB)
Collecting aiosignal==1.3.1 (from scenicplus==1.0a1)
  Using cached aiosignal-1.3.1-py3-none-any.whl.metadata (4.0 kB)
Collecting anndata==0.10.5.post1 (from scenicplus==1.0a1)
  Using cached anndata-0.10.5.post1-py3-none-any.whl.metadata (6.5 kB)
Collecting annoy==1.17.3 (from scenicplus==1.0a1)
  Using cached annoy-1.17.3-cp311-cp311-linux_x86_64.whl
Collecting appdirs==1.4.4 (from scenicplus==1.0a1)
  Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting arboreto==0.1.6 (from scenicplus==1.0a1)
  Using cached arboreto-0.1.6-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting argparse-dataclass==2.0.0 (from scenicplus==1.0a1)
  Using cached argparse_dataclass-2.0.0-py3-none-any.whl.metadata (7.2 kB)
Collecting array-api-compat==1.5.1 (from scenicplus==1.0a1)
  Using cached array_api_compat-1.5.1-py3-none-any.whl.metadata (1.3 kB)
Collecting asttokens==2.4.1 (from scenicplus==1.0a1)
  Using cached asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting attr==0.3.2 (from scenicplus==1.0a1)
  Using cached attr-0.3.2-py2.py3-none-any.whl.metadata (1.2 kB)
Collecting attrs==23.2.0 (from scenicplus==1.0a1)
  Using cached attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB)
Collecting bbknn==1.6.0 (from scenicplus==1.0a1)
  Using cached bbknn-1.6.0-py3-none-any.whl.metadata (8.2 kB)
Collecting beautifulsoup4==4.12.3 (from scenicplus==1.0a1)
  Using cached beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting bidict==0.23.1 (from scenicplus==1.0a1)
  Using cached bidict-0.23.1-py3-none-any.whl.metadata (8.7 kB)
Collecting bioservices==1.11.2 (from scenicplus==1.0a1)
  Using cached bioservices-1.11.2-py3-none-any.whl
Collecting blosc2==2.5.1 (from scenicplus==1.0a1)
  Using cached blosc2-2.5.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
Collecting bokeh==3.4.0 (from scenicplus==1.0a1)
  Using cached bokeh-3.4.0-py3-none-any.whl.metadata (12 kB)
Collecting boltons==23.1.1 (from scenicplus==1.0a1)
  Using cached boltons-23.1.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting bs4==0.0.2 (from scenicplus==1.0a1)
  Using cached bs4-0.0.2-py2.py3-none-any.whl.metadata (411 bytes)
Collecting cattrs==23.2.3 (from scenicplus==1.0a1)
  Using cached cattrs-23.2.3-py3-none-any.whl.metadata (10 kB)
Collecting certifi==2024.2.2 (from scenicplus==1.0a1)
  Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting charset-normalizer==3.3.2 (from scenicplus==1.0a1)
  Using cached charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting click==8.1.7 (from scenicplus==1.0a1)
  Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting cloudpickle==3.0.0 (from scenicplus==1.0a1)
  Using cached cloudpickle-3.0.0-py3-none-any.whl.metadata (7.0 kB)
Collecting colorama==0.4.6 (from scenicplus==1.0a1)
  Using cached colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)
Collecting colorlog==6.8.2 (from scenicplus==1.0a1)
  Using cached colorlog-6.8.2-py3-none-any.whl.metadata (10 kB)
Collecting conda-inject==1.3.1 (from scenicplus==1.0a1)
  Using cached conda_inject-1.3.1-py3-none-any.whl.metadata (855 bytes)
Collecting configargparse==1.7 (from scenicplus==1.0a1)
  Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB)
Collecting connection-pool==0.0.3 (from scenicplus==1.0a1)
  Using cached connection_pool-0.0.3-py3-none-any.whl
Requirement already satisfied: contourpy==1.2.0 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (1.2.0)
Collecting ctxcore==0.2.0 (from scenicplus==1.0a1)
  Using cached ctxcore-0.2.0-py3-none-any.whl.metadata (3.1 kB)
Requirement already satisfied: cycler==0.12.1 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (0.12.1)
Collecting cython==0.29.37 (from scenicplus==1.0a1)
  Using cached Cython-0.29.37-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.1 kB)
Collecting cytoolz==0.12.3 (from scenicplus==1.0a1)
  Using cached cytoolz-0.12.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.6 kB)
Collecting dask==2024.2.1 (from dask[array,complete,dataframe,diagnostics,distributed]==2024.2.1->scenicplus==1.0a1)
  Using cached dask-2024.2.1-py3-none-any.whl.metadata (3.7 kB)
Collecting dataclasses-json==0.6.4 (from scenicplus==1.0a1)
  Using cached dataclasses_json-0.6.4-py3-none-any.whl.metadata (25 kB)
Collecting datrie==0.8.2 (from scenicplus==1.0a1)
  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 decorator==5.1.1 (from scenicplus==1.0a1)
  Using cached decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting dill==0.3.8 (from scenicplus==1.0a1)
  Using cached dill-0.3.8-py3-none-any.whl.metadata (10 kB)
Collecting distributed==2024.2.1 (from scenicplus==1.0a1)
  Using cached distributed-2024.2.1-py3-none-any.whl.metadata (3.4 kB)
Collecting docutils==0.20.1 (from scenicplus==1.0a1)
  Using cached docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Collecting dpath==2.1.6 (from scenicplus==1.0a1)
  Using cached dpath-2.1.6-py3-none-any.whl.metadata (15 kB)
Collecting easydev==0.13.1 (from scenicplus==1.0a1)
  Using cached easydev-0.13.1-py3-none-any.whl.metadata (3.5 kB)
Collecting et-xmlfile==1.1.0 (from scenicplus==1.0a1)
  Using cached et_xmlfile-1.1.0-py3-none-any.whl.metadata (1.8 kB)
Collecting executing==2.0.1 (from scenicplus==1.0a1)
  Using cached executing-2.0.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting fastjsonschema==2.19.1 (from scenicplus==1.0a1)
  Using cached fastjsonschema-2.19.1-py3-none-any.whl.metadata (2.1 kB)
Collecting fbpca==1.0 (from scenicplus==1.0a1)
  Using cached fbpca-1.0-py3-none-any.whl
Collecting filelock==3.13.1 (from scenicplus==1.0a1)
  Using cached filelock-3.13.1-py3-none-any.whl.metadata (2.8 kB)
Collecting fonttools==4.50.0 (from scenicplus==1.0a1)
  Using cached fonttools-4.50.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB)
Collecting frozendict==2.4.0 (from scenicplus==1.0a1)
  Using cached frozendict-2.4.0-py3-none-any.whl
Collecting frozenlist==1.4.1 (from scenicplus==1.0a1)
  Using cached frozenlist-1.4.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting fsspec==2024.3.1 (from scenicplus==1.0a1)
  Using cached fsspec-2024.3.1-py3-none-any.whl.metadata (6.8 kB)
Collecting future==1.0.0 (from scenicplus==1.0a1)
  Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting gensim==4.3.2 (from scenicplus==1.0a1)
  Using cached gensim-4.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.3 kB)
Collecting geosketch==1.2 (from scenicplus==1.0a1)
  Using cached geosketch-1.2-py3-none-any.whl.metadata (406 bytes)
Collecting gevent==24.2.1 (from scenicplus==1.0a1)
  Using cached gevent-24.2.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (13 kB)
Collecting gitdb==4.0.11 (from scenicplus==1.0a1)
  Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting gitpython==3.1.42 (from scenicplus==1.0a1)
  Using cached GitPython-3.1.42-py3-none-any.whl.metadata (12 kB)
Collecting globre==0.1.5 (from scenicplus==1.0a1)
  Using cached globre-0.1.5-py3-none-any.whl
Collecting greenlet==3.0.3 (from scenicplus==1.0a1)
  Using cached greenlet-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB)
Collecting grequests==0.7.0 (from scenicplus==1.0a1)
  Using cached grequests-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting gseapy==0.10.8 (from scenicplus==1.0a1)
  Using cached gseapy-0.10.8-py3-none-any.whl.metadata (11 kB)
Requirement already satisfied: h5py==3.10.0 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (3.10.0)
Collecting harmonypy==0.0.9 (from scenicplus==1.0a1)
  Using cached harmonypy-0.0.9-py3-none-any.whl.metadata (3.7 kB)
Collecting humanfriendly==10.0 (from scenicplus==1.0a1)
  Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Collecting idna==3.6 (from scenicplus==1.0a1)
  Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting igraph==0.11.4 (from scenicplus==1.0a1)
  Using cached igraph-0.11.4-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Collecting imageio==2.34.0 (from scenicplus==1.0a1)
  Using cached imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB)
Collecting immutables==0.20 (from scenicplus==1.0a1)
  Using cached immutables-0.20-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.6 kB)
Collecting importlib-metadata==7.0.1 (from scenicplus==1.0a1)
  Using cached importlib_metadata-7.0.1-py3-none-any.whl.metadata (4.9 kB)
Collecting importlib-resources==6.1.2 (from scenicplus==1.0a1)
  Using cached importlib_resources-6.1.2-py3-none-any.whl.metadata (3.9 kB)
Collecting interlap==0.2.7 (from scenicplus==1.0a1)
  Using cached interlap-0.2.7-py3-none-any.whl
Collecting intervaltree==3.1.0 (from scenicplus==1.0a1)
  Using cached intervaltree-3.1.0-py2.py3-none-any.whl
Collecting ipython==8.22.2 (from scenicplus==1.0a1)
  Using cached ipython-8.22.2-py3-none-any.whl.metadata (4.8 kB)
Collecting jedi==0.19.1 (from scenicplus==1.0a1)
  Using cached jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting jinja2==3.1.3 (from scenicplus==1.0a1)
  Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
Requirement already satisfied: joblib==1.3.2 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (1.3.2)
Collecting jsonpickle==3.0.3 (from scenicplus==1.0a1)
  Using cached jsonpickle-3.0.3-py3-none-any.whl.metadata (7.3 kB)
Collecting jsonschema==4.21.1 (from scenicplus==1.0a1)
  Using cached jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB)
Collecting jsonschema-specifications==2023.12.1 (from scenicplus==1.0a1)
  Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)
Collecting jupyter-core==5.7.2 (from scenicplus==1.0a1)
  Using cached jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting kaleido==0.2.1 (from scenicplus==1.0a1)
  Using cached kaleido-0.2.1-py2.py3-none-manylinux1_x86_64.whl.metadata (15 kB)
Requirement already satisfied: kiwisolver==1.4.5 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (1.4.5)
Collecting lazy-loader==0.3 (from scenicplus==1.0a1)
  Using cached lazy_loader-0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting lda==3.0.0 (from scenicplus==1.0a1)
  Using cached lda-3.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)
Collecting leidenalg==0.10.2 (from scenicplus==1.0a1)
  Using cached leidenalg-0.10.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting line-profiler==4.1.2 (from scenicplus==1.0a1)
  Using cached line_profiler-4.1.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB)
Collecting llvmlite==0.42.0 (from scenicplus==1.0a1)
  Using cached llvmlite-0.42.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB)
Collecting locket==1.0.0 (from scenicplus==1.0a1)
  Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
Collecting loompy==3.0.7 (from scenicplus==1.0a1)
  Using cached loompy-3.0.7-py3-none-any.whl
Collecting lxml==5.1.0 (from scenicplus==1.0a1)
  Using cached lxml-5.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.5 kB)
Collecting lz4==4.3.3 (from scenicplus==1.0a1)
  Using cached lz4-4.3.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.7 kB)
Collecting macs2==2.2.9.1 (from scenicplus==1.0a1)
  Using cached MACS2-2.2.9.1-cp311-cp311-linux_x86_64.whl
Collecting markdown-it-py==3.0.0 (from scenicplus==1.0a1)
  Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting markupsafe==2.1.5 (from scenicplus==1.0a1)
  Using cached MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting marshmallow==3.21.1 (from scenicplus==1.0a1)
  Using cached marshmallow-3.21.1-py3-none-any.whl.metadata (7.2 kB)
Collecting matplotlib==3.6.3 (from scenicplus==1.0a1)
  Using cached matplotlib-3.6.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB)
Collecting matplotlib-inline==0.1.6 (from scenicplus==1.0a1)
  Using cached matplotlib_inline-0.1.6-py3-none-any.whl.metadata (2.8 kB)
Collecting mdurl==0.1.2 (from scenicplus==1.0a1)
  Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting mizani==0.9.3 (from scenicplus==1.0a1)
  Using cached mizani-0.9.3-py3-none-any.whl.metadata (4.6 kB)
Collecting msgpack==1.0.8 (from scenicplus==1.0a1)
  Using cached msgpack-1.0.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Collecting mudata==0.2.3 (from scenicplus==1.0a1)
  Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB)
Collecting multidict==6.0.5 (from scenicplus==1.0a1)
  Using cached multidict-6.0.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)
Collecting multiprocessing-on-dill==3.5.0a4 (from scenicplus==1.0a1)
  Using cached multiprocessing_on_dill-3.5.0a4-py3-none-any.whl
Collecting mypy-extensions==1.0.0 (from scenicplus==1.0a1)
  Using cached mypy_extensions-1.0.0-py3-none-any.whl.metadata (1.1 kB)
Requirement already satisfied: natsort==8.4.0 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (8.4.0)
Collecting nbformat==5.10.3 (from scenicplus==1.0a1)
  Using cached nbformat-5.10.3-py3-none-any.whl.metadata (3.6 kB)
Collecting ncls==0.0.68 (from scenicplus==1.0a1)
  Using cached ncls-0.0.68-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.6 kB)
Collecting ndindex==1.8 (from scenicplus==1.0a1)
  Using cached ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)
Requirement already satisfied: networkx==3.2.1 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (3.2.1)
Collecting numba==0.59.0 (from scenicplus==1.0a1)
  Using cached numba-0.59.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting numexpr==2.9.0 (from scenicplus==1.0a1)
  Using cached numexpr-2.9.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
Collecting numpy==1.26.4 (from scenicplus==1.0a1)
  Using cached numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Collecting numpy-groupies==0.10.2 (from scenicplus==1.0a1)
  Using cached numpy_groupies-0.10.2-py3-none-any.whl.metadata (18 kB)
Collecting openpyxl==3.1.2 (from scenicplus==1.0a1)
  Using cached openpyxl-3.1.2-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting packaging==24.0 (from scenicplus==1.0a1)
  Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
Collecting pandas==1.5.0 (from scenicplus==1.0a1)
  Using cached pandas-1.5.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting parso==0.8.3 (from scenicplus==1.0a1)
  Using cached parso-0.8.3-py2.py3-none-any.whl.metadata (7.5 kB)
Collecting partd==1.4.1 (from scenicplus==1.0a1)
  Using cached partd-1.4.1-py3-none-any.whl.metadata (4.6 kB)
Collecting patsy==0.5.6 (from scenicplus==1.0a1)
  Using cached patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting pexpect==4.9.0 (from scenicplus==1.0a1)
  Using cached pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Requirement already satisfied: pillow==10.2.0 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (10.2.0)
Collecting plac==1.4.3 (from scenicplus==1.0a1)
  Using cached plac-1.4.3-py2.py3-none-any.whl.metadata (5.9 kB)
Collecting platformdirs==4.2.0 (from scenicplus==1.0a1)
  Using cached platformdirs-4.2.0-py3-none-any.whl.metadata (11 kB)
Collecting plotly==5.19.0 (from scenicplus==1.0a1)
  Using cached plotly-5.19.0-py3-none-any.whl.metadata (7.0 kB)
Collecting plotnine==0.12.4 (from scenicplus==1.0a1)
  Using cached plotnine-0.12.4-py3-none-any.whl.metadata (8.9 kB)
Collecting polars==0.20.13 (from scenicplus==1.0a1)
  Using cached polars-0.20.13-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (15 kB)
Collecting progressbar2==4.4.2 (from scenicplus==1.0a1)
  Using cached progressbar2-4.4.2-py3-none-any.whl.metadata (17 kB)
Collecting prompt-toolkit==3.0.43 (from scenicplus==1.0a1)
  Using cached prompt_toolkit-3.0.43-py3-none-any.whl.metadata (6.5 kB)
Collecting protobuf==5.26.0 (from scenicplus==1.0a1)
  Using cached protobuf-5.26.0-cp37-abi3-manylinux2014_x86_64.whl.metadata (592 bytes)
Collecting psutil==5.9.8 (from scenicplus==1.0a1)
  Using cached psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting ptyprocess==0.7.0 (from scenicplus==1.0a1)
  Using cached ptyprocess-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting pulp==2.8.0 (from scenicplus==1.0a1)
  Using cached PuLP-2.8.0-py3-none-any.whl.metadata (5.4 kB)
Collecting pure-eval==0.2.2 (from scenicplus==1.0a1)
  Using cached pure_eval-0.2.2-py3-none-any.whl.metadata (6.2 kB)
Collecting py-cpuinfo==9.0.0 (from scenicplus==1.0a1)
  Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
Collecting pyarrow==15.0.0 (from scenicplus==1.0a1)
  Using cached pyarrow-15.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 kB)
Collecting pyarrow-hotfix==0.6 (from scenicplus==1.0a1)
  Using cached pyarrow_hotfix-0.6-py3-none-any.whl.metadata (3.6 kB)
Collecting pybedtools==0.9.1 (from scenicplus==1.0a1)
  Using cached pybedtools-0.9.1-cp311-cp311-linux_x86_64.whl
Collecting pybigtools==0.1.2 (from scenicplus==1.0a1)
  Using cached pybigtools-0.1.2-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (1.2 kB)
Collecting pybigwig==0.3.22 (from scenicplus==1.0a1)
  Using cached pyBigWig-0.3.22-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting pybiomart==0.2.0 (from scenicplus==1.0a1)
  Using cached pybiomart-0.2.0-py3-none-any.whl.metadata (1.1 kB)
Collecting pyfasta==0.5.2 (from scenicplus==1.0a1)
  Using cached pyfasta-0.5.2-py3-none-any.whl
Collecting pygam==0.9.0 (from scenicplus==1.0a1)
  Using cached pygam-0.9.0-py3-none-any.whl.metadata (7.0 kB)
Collecting pygments==2.17.2 (from scenicplus==1.0a1)
  Using cached pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB)
Collecting pynndescent==0.5.11 (from scenicplus==1.0a1)
  Using cached pynndescent-0.5.11-py3-none-any.whl.metadata (6.8 kB)
Collecting pyparsing==3.1.2 (from scenicplus==1.0a1)
  Using cached pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)
Collecting pyranges==0.0.111 (from scenicplus==1.0a1)
  Using cached pyranges-0.0.111-py3-none-any.whl
Collecting pyrle==0.0.39 (from scenicplus==1.0a1)
  Using cached pyrle-0.0.39-cp311-cp311-linux_x86_64.whl
Requirement already satisfied: pysam==0.22.0 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (0.22.0)
Collecting python-dateutil==2.9.0.post0 (from scenicplus==1.0a1)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting python-utils==3.8.2 (from scenicplus==1.0a1)
  Using cached python_utils-3.8.2-py2.py3-none-any.whl.metadata (9.7 kB)
Collecting pytz==2024.1 (from scenicplus==1.0a1)
  Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting pyvis==0.3.2 (from scenicplus==1.0a1)
  Using cached pyvis-0.3.2-py3-none-any.whl.metadata (1.7 kB)
Collecting pyyaml==6.0.1 (from scenicplus==1.0a1)
  Using cached PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting ray==2.9.3 (from scenicplus==1.0a1)
  Using cached ray-2.9.3-cp311-cp311-manylinux2014_x86_64.whl.metadata (13 kB)
Collecting referencing==0.34.0 (from scenicplus==1.0a1)
  Using cached referencing-0.34.0-py3-none-any.whl.metadata (2.8 kB)
Collecting requests==2.31.0 (from scenicplus==1.0a1)
  Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting requests-cache==1.2.0 (from scenicplus==1.0a1)
  Using cached requests_cache-1.2.0-py3-none-any.whl.metadata (9.9 kB)
Collecting reretry==0.11.8 (from scenicplus==1.0a1)
  Using cached reretry-0.11.8-py2.py3-none-any.whl.metadata (5.5 kB)
Collecting rich==13.7.1 (from scenicplus==1.0a1)
  Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting rich-argparse==1.4.0 (from scenicplus==1.0a1)
  Using cached rich_argparse-1.4.0-py3-none-any.whl.metadata (14 kB)
Collecting rpds-py==0.18.0 (from scenicplus==1.0a1)
  Using cached rpds_py-0.18.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
Collecting scanorama==1.7.4 (from scenicplus==1.0a1)
  Using cached scanorama-1.7.4-py3-none-any.whl.metadata (525 bytes)
Collecting scanpy==1.8.2 (from scenicplus==1.0a1)
  Using cached scanpy-1.8.2-py3-none-any.whl.metadata (5.8 kB)
Collecting scatac-fragment-tools==0.1.0 (from scenicplus==1.0a1)
  Using cached scatac_fragment_tools-0.1.0-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.6 kB)
Collecting scikit-image==0.22.0 (from scenicplus==1.0a1)
  Using cached scikit_image-0.22.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scikit-learn==1.3.2 (from scenicplus==1.0a1)
  Using cached scikit_learn-1.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting scipy==1.12.0 (from scenicplus==1.0a1)
  Using cached scipy-1.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting scrublet==0.2.3 (from scenicplus==1.0a1)
  Using cached scrublet-0.2.3-py3-none-any.whl.metadata (3.1 kB)
Requirement already satisfied: seaborn==0.13.2 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (0.13.2)
Collecting sinfo==0.3.4 (from scenicplus==1.0a1)
  Using cached sinfo-0.3.4-py3-none-any.whl
Collecting six==1.16.0 (from scenicplus==1.0a1)
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting smart-open==6.4.0 (from scenicplus==1.0a1)
  Using cached smart_open-6.4.0-py3-none-any.whl.metadata (21 kB)
Collecting smmap==5.0.1 (from scenicplus==1.0a1)
  Using cached smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Collecting snakemake==8.5.5 (from scenicplus==1.0a1)
  Using cached snakemake-8.5.5-py3-none-any.whl.metadata (2.5 kB)
Collecting snakemake-interface-common==1.17.1 (from scenicplus==1.0a1)
  Using cached snakemake_interface_common-1.17.1-py3-none-any.whl.metadata (760 bytes)
Collecting snakemake-interface-executor-plugins==8.2.0 (from scenicplus==1.0a1)
  Using cached snakemake_interface_executor_plugins-8.2.0-py3-none-any.whl.metadata (7.7 kB)
Collecting snakemake-interface-report-plugins==1.0.0 (from scenicplus==1.0a1)
  Using cached snakemake_interface_report_plugins-1.0.0-py3-none-any.whl.metadata (3.4 kB)
Collecting snakemake-interface-storage-plugins==3.1.1 (from scenicplus==1.0a1)
  Using cached snakemake_interface_storage_plugins-3.1.1-py3-none-any.whl.metadata (9.4 kB)
Collecting sorted-nearest==0.0.39 (from scenicplus==1.0a1)
  Using cached sorted_nearest-0.0.39-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (964 bytes)
Collecting sortedcontainers==2.4.0 (from scenicplus==1.0a1)
  Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting soupsieve==2.5 (from scenicplus==1.0a1)
  Using cached soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB)
Collecting stack-data==0.6.3 (from scenicplus==1.0a1)
  Using cached stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting statistics==1.0.3.5 (from scenicplus==1.0a1)
  Using cached statistics-1.0.3.5-py3-none-any.whl
Collecting statsmodels==0.14.1 (from scenicplus==1.0a1)
  Using cached statsmodels-0.14.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.5 kB)
Collecting stdlib-list==0.10.0 (from scenicplus==1.0a1)
  Using cached stdlib_list-0.10.0-py3-none-any.whl.metadata (3.3 kB)
Collecting stopit==1.1.2 (from scenicplus==1.0a1)
  Using cached stopit-1.1.2-py3-none-any.whl
Collecting suds-community==1.1.2 (from scenicplus==1.0a1)
  Using cached suds_community-1.1.2-py3-none-any.whl.metadata (1.7 kB)
Collecting tables==3.9.2 (from scenicplus==1.0a1)
  Using cached tables-3.9.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting tabulate==0.9.0 (from scenicplus==1.0a1)
  Using cached tabulate-0.9.0-py3-none-any.whl.metadata (34 kB)
Collecting tblib==3.0.0 (from scenicplus==1.0a1)
  Using cached tblib-3.0.0-py3-none-any.whl.metadata (25 kB)
Collecting tenacity==8.2.3 (from scenicplus==1.0a1)
  Using cached tenacity-8.2.3-py3-none-any.whl.metadata (1.0 kB)
Collecting texttable==1.7.0 (from scenicplus==1.0a1)
  Using cached texttable-1.7.0-py2.py3-none-any.whl.metadata (9.8 kB)
Collecting threadpoolctl==3.4.0 (from scenicplus==1.0a1)
  Using cached threadpoolctl-3.4.0-py3-none-any.whl.metadata (13 kB)
Collecting throttler==1.2.2 (from scenicplus==1.0a1)
  Using cached throttler-1.2.2-py3-none-any.whl.metadata (7.4 kB)
Collecting tifffile==2024.2.12 (from scenicplus==1.0a1)
  Using cached tifffile-2024.2.12-py3-none-any.whl.metadata (31 kB)
Collecting tmtoolkit==0.12.0 (from scenicplus==1.0a1)
  Using cached tmtoolkit-0.12.0-py3-none-any.whl.metadata (14 kB)
Collecting toolz==0.12.1 (from scenicplus==1.0a1)
  Using cached toolz-0.12.1-py3-none-any.whl.metadata (5.1 kB)
Collecting toposort==1.10 (from scenicplus==1.0a1)
  Using cached toposort-1.10-py3-none-any.whl.metadata (4.1 kB)
Collecting tornado==6.4 (from scenicplus==1.0a1)
  Using cached tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Requirement already satisfied: tqdm==4.66.2 in /u/cdslab/astacchetti/.local/lib/python3.11/site-packages (from scenicplus==1.0a1) (4.66.2)
Collecting traitlets==5.14.2 (from scenicplus==1.0a1)
  Using cached traitlets-5.14.2-py3-none-any.whl.metadata (10 kB)
Collecting tspex==0.6.3 (from scenicplus==1.0a1)
  Using cached tspex-0.6.3-py3-none-any.whl
Collecting typing==3.7.4.3 (from scenicplus==1.0a1)
  Using cached typing-3.7.4.3-py3-none-any.whl
Collecting typing-extensions==4.10.0 (from scenicplus==1.0a1)
  Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB)
Collecting typing-inspect==0.9.0 (from scenicplus==1.0a1)
  Using cached typing_inspect-0.9.0-py3-none-any.whl.metadata (1.5 kB)
Collecting umap-learn==0.5.5 (from scenicplus==1.0a1)
  Using cached umap_learn-0.5.5-py3-none-any.whl
Collecting url-normalize==1.4.3 (from scenicplus==1.0a1)
  Using cached url_normalize-1.4.3-py2.py3-none-any.whl.metadata (3.1 kB)
Collecting urllib3==2.2.1 (from scenicplus==1.0a1)
  Using cached urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB)
Collecting wcwidth==0.2.13 (from scenicplus==1.0a1)
  Using cached wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB)
Collecting wheel==0.43.0 (from scenicplus==1.0a1)
  Using cached wheel-0.43.0-py3-none-any.whl.metadata (2.2 kB)
Collecting wrapt==1.16.0 (from scenicplus==1.0a1)
  Using cached wrapt-1.16.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting xlrd==2.0.1 (from scenicplus==1.0a1)
  Using cached xlrd-2.0.1-py2.py3-none-any.whl.metadata (3.4 kB)
Collecting xmltodict==0.13.0 (from scenicplus==1.0a1)
  Using cached xmltodict-0.13.0-py2.py3-none-any.whl.metadata (7.7 kB)
Collecting xyzservices==2023.10.1 (from scenicplus==1.0a1)
  Using cached xyzservices-2023.10.1-py3-none-any.whl.metadata (4.0 kB)
Collecting yarl==1.9.4 (from scenicplus==1.0a1)
  Using cached yarl-1.9.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB)
Collecting yte==1.5.4 (from scenicplus==1.0a1)
  Using cached yte-1.5.4-py3-none-any.whl.metadata (3.4 kB)
Collecting zict==3.0.0 (from scenicplus==1.0a1)
  Using cached zict-3.0.0-py2.py3-none-any.whl.metadata (899 bytes)
Collecting zipp==3.18.1 (from scenicplus==1.0a1)
  Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
Collecting zope-event==5.0 (from scenicplus==1.0a1)
  Using cached zope.event-5.0-py3-none-any.whl.metadata (4.4 kB)
Collecting zope-interface==6.2 (from scenicplus==1.0a1)
  Using cached zope.interface-6.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (41 kB)
Requirement already satisfied: setuptools in /u/cdslab/astacchetti/miniconda3/envs/scenicplus/lib/python3.11/site-packages (from loompy==3.0.7->scenicplus==1.0a1) (73.0.1)
Using cached adjustText-1.0.4-py3-none-any.whl (11 kB)
Using cached aiohttp-3.9.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB)
Using cached anndata-0.10.5.post1-py3-none-any.whl (121 kB)
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Using cached arboreto-0.1.6-py2.py3-none-any.whl (15 kB)
Using cached argparse_dataclass-2.0.0-py3-none-any.whl (8.8 kB)
Using cached array_api_compat-1.5.1-py3-none-any.whl (35 kB)
Using cached asttokens-2.4.1-py2.py3-none-any.whl (27 kB)
Using cached attr-0.3.2-py2.py3-none-any.whl (3.3 kB)
Using cached attrs-23.2.0-py3-none-any.whl (60 kB)
Using cached bbknn-1.6.0-py3-none-any.whl (14 kB)
Using cached beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Using cached bidict-0.23.1-py3-none-any.whl (32 kB)
Using cached blosc2-2.5.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
Using cached bokeh-3.4.0-py3-none-any.whl (7.0 MB)
Using cached boltons-23.1.1-py2.py3-none-any.whl (195 kB)
Using cached bs4-0.0.2-py2.py3-none-any.whl (1.2 kB)
Using cached cattrs-23.2.3-py3-none-any.whl (57 kB)
Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
Using cached charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (140 kB)
Using cached click-8.1.7-py3-none-any.whl (97 kB)
Using cached cloudpickle-3.0.0-py3-none-any.whl (20 kB)
Using cached colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Using cached colorlog-6.8.2-py3-none-any.whl (11 kB)
Using cached conda_inject-1.3.1-py3-none-any.whl (4.1 kB)
Using cached ConfigArgParse-1.7-py3-none-any.whl (25 kB)
Using cached ctxcore-0.2.0-py3-none-any.whl (5.8 MB)
Using cached Cython-0.29.37-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Using cached cytoolz-0.12.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
Using cached dask-2024.2.1-py3-none-any.whl (1.2 MB)
Using cached dataclasses_json-0.6.4-py3-none-any.whl (28 kB)
Using cached decorator-5.1.1-py3-none-any.whl (9.1 kB)
Using cached dill-0.3.8-py3-none-any.whl (116 kB)
Using cached distributed-2024.2.1-py3-none-any.whl (1.0 MB)
Using cached docutils-0.20.1-py3-none-any.whl (572 kB)
Using cached dpath-2.1.6-py3-none-any.whl (17 kB)
Using cached easydev-0.13.1-py3-none-any.whl (56 kB)
Using cached et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
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Building wheels for collected packages: scenicplus, datrie, loomxpy, pyscenic, pycistarget, pycistopic
  Building wheel for scenicplus (pyproject.toml) ... done
  Created wheel for scenicplus: filename=scenicplus-1.0a1-py3-none-any.whl size=143467 sha256=6ba432e21e1d0f9851a0bc54cb349d27717e643b2d42325447886bd201444064
  Stored in directory: /tmp/pip-ephem-wheel-cache-gvvtxku7/wheels/53/eb/af/50658a460f46fa411b6db8035918416047c40e5ce183a07e42
  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
  ╰─> [77 lines of output]
      /tmp/pip-build-env-daiym57f/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
        warnings.warn(msg)
      running bdist_wheel
      running build
      running build_clib
      building 'datrie' library
      creating build
      creating build/temp.linux-x86_64-cpython-311
      creating build/temp.linux-x86_64-cpython-311/libdatrie
      creating build/temp.linux-x86_64-cpython-311/libdatrie/datrie
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/alpha-map.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/darray.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/darray.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/dstring.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/dstring.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/fileutils.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/fileutils.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/tail.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/tail.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/trie-string.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie-string.o
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -c libdatrie/datrie/trie.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie.o
      ar rcs build/temp.linux-x86_64-cpython-311/libdatrie.a build/temp.linux-x86_64-cpython-311/libdatrie/datrie/alpha-map.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/darray.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/dstring.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/fileutils.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/tail.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie-string.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie.o
      running build_ext
      building 'datrie' extension
      creating build/temp.linux-x86_64-cpython-311/src
      gcc -pthread -B /u/cdslab/astacchetti/miniconda3/envs/scenicplus/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -O2 -isystem /u/cdslab/astacchetti/miniconda3/envs/scenicplus/include -fPIC -Ilibdatrie -I/u/cdslab/astacchetti/miniconda3/envs/scenicplus/include/python3.11 -c src/datrie.c -o build/temp.linux-x86_64-cpython-311/src/datrie.o
      src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie___init__’:
      src/datrie.c:5669:53: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
       5669 |   __pyx_v_self->_c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
            |                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                     |
            |                                                     struct AlphaMap *
      In file included from src/datrie.c:1248:
      src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
        120 | Trie *  trie_new (const AlphaMap *alpha_map);
            |                   ~~~~~~~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie_6clear’:
      src/datrie.c:6347:47: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
       6347 |   __pyx_v__c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
            |                              ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                               |
            |                                               struct AlphaMap *
      src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
        120 | Trie *  trie_new (const AlphaMap *alpha_map);
            |                   ~~~~~~~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap___cinit__’:
      src/datrie.c:27405:30: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
      27405 |   __pyx_v_self->_c_alpha_map = alpha_map_new();
            |                              ^
      src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap_2__dealloc__’:
      src/datrie.c:27461:32: error: passing argument 1 of ‘alpha_map_free’ from incompatible pointer type [-Wincompatible-pointer-types]
      27461 |     alpha_map_free(__pyx_v_self->_c_alpha_map);
            |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                |
            |                                struct AlphaMap *
      In file included from src/datrie.c:1247:
      src/../libdatrie/datrie/alpha-map.h:72:39: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         72 | void        alpha_map_free (AlphaMap *alpha_map);
            |                             ~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap_copy’:
      src/datrie.c:27876:61: error: passing argument 1 of ‘alpha_map_clone’ from incompatible pointer type [-Wincompatible-pointer-types]
      27876 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
            |                                                 ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                             |
            |                                                             struct AlphaMap *
      src/../libdatrie/datrie/alpha-map.h:70:46: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         70 | AlphaMap *  alpha_map_clone (const AlphaMap *a_map);
            |                              ~~~~~~~~~~~~~~~~^~~~~
      src/datrie.c:27876:31: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
      27876 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
            |                               ^
      src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap__add_range’:
      src/datrie.c:28567:50: error: passing argument 1 of ‘alpha_map_add_range’ from incompatible pointer type [-Wincompatible-pointer-types]
      28567 |   __pyx_v_code = alpha_map_add_range(__pyx_v_self->_c_alpha_map, __pyx_v_begin, __pyx_v_end);
            |                                      ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                  |
            |                                                  struct AlphaMap *
      src/../libdatrie/datrie/alpha-map.h:74:45: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         74 | int         alpha_map_add_range (AlphaMap  *alpha_map,
            |                                  ~~~~~~~~~~~^~~~~~~~~
      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
  Building wheel for loomxpy (pyproject.toml) ... done
  Created wheel for loomxpy: filename=loomxpy-0.4.2-py3-none-any.whl size=28480 sha256=8b156566298251ee18a3f08bb0250dbaeea721b888f0c87c6586b8fdd9310c23
  Stored in directory: /tmp/pip-ephem-wheel-cache-gvvtxku7/wheels/7a/3a/8a/21d26a485464c1c66d81da84ae8c8536ebf9629f2d4ec480da
  Building wheel for pyscenic (setup.py) ... done
  Created wheel for pyscenic: filename=pyscenic-0.12.1+8.gd2309fe-py3-none-any.whl size=7100116 sha256=6644eabc220774545a3a7346298b0cfd38d7fc78df468e4545bd0a20d0b94e34
  Stored in directory: /tmp/pip-ephem-wheel-cache-gvvtxku7/wheels/34/b0/cc/4961f5e29900a4e897551d3390658f02f1f34d13813d49b852
  Building wheel for pycistarget (pyproject.toml) ... done
  Created wheel for pycistarget: filename=pycistarget-1.0a2-py3-none-any.whl size=29091 sha256=afe8d1c5c7a7b22ac2dd94ddff693c243686813ed9d8362811126a5eda6a8274
  Stored in directory: /tmp/pip-ephem-wheel-cache-gvvtxku7/wheels/9e/f3/f1/783c17fdf05516179f2f66a088ea6b41ab2c7d8afe8e40e090
  Building wheel for pycistopic (pyproject.toml) ... done
  Created wheel for pycistopic: filename=pycisTopic-2.0a0-py3-none-any.whl size=125305 sha256=1b03a4fae67f9f1e1688280fb1e1d5bf546627b2f84b6bb7ffe7128a5099275c
  Stored in directory: /tmp/pip-ephem-wheel-cache-gvvtxku7/wheels/c1/c7/24/a73f70fa0e8797e75a8feaad32c6ad3730d8ca2b6809158ca0
Successfully built scenicplus loomxpy pyscenic pycistarget pycistopic
Failed to build datrie
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (datrie)

Expected behavior I expected I could installing without havung so many troubles

Additional context I also tried pip install -r requirements.txt , but nothing changes

ghuls commented 1 week ago

which version of GCC and pip do you have?

Stack7 commented 1 week ago

this is my version of gcc:(GCC) 14.2.1 20240801 (Red Hat 14.2.1-1). it seems like there is a missed reference of a pointer in the error For pip the version is the following: pip 24.2, however I tried with pip 24.1, 24.0 and 23.3.2 and nothing has changed

ghuls commented 1 week ago

Seems to be a known issue with datrie and GCC 14: https://github.com/pytries/datrie/issues/101

You will have to download datrie source code and patch one file: https://github.com/pytries/datrie/pull/99 And then install that version.