search

KChen-lab / SCMER

Marker Selection by matching manifolds and elastic net
https://scmer.readthedocs.io/
MIT License
23 stars 4 forks source link

error installing scmer #3

Closed Kur1sutaru closed 1 year ago

Kur1sutaru commented 1 year ago

I tried in several machines install scmer but I get this error:

ERROR: Failed cleaning build dir for numpy
      Failed to build numpy
      ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects
      [end of output]

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

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

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

I want to know which requirements we need, in the requirements file we have only the scikit-learn version, could you please provide the correct versions for torch, numpy, scipy, pandas, and seaborn?

Thanks a lot! 😄

Kur1sutaru commented 1 year ago

tks

lshh125 commented 1 year ago

Hi. I guess you might have figured it out. Here are my latest working system & package info in case it is helpful to you or others.

Please don't hesitate to contact me if you have any other questions.

System: Ubuntu 20.04.5 LTS (5.15.0-73-generic) GPU: RTX 3080 (NVIDIA-SMI 515.105.01 Driver Version: 515.105.01 CUDA Version: 11.7 )

Conda environment: _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge anndata 0.8.0 pyhd8ed1ab_1 conda-forge anyio 3.5.0 py39h06a4308_0
argon2-cffi 20.1.0 py39h27cfd23_1
arpack 3.7.0 hc6cf775_2 conda-forge asttokens 2.0.5 pyhd3eb1b0_0
attrs 21.4.0 pyhd3eb1b0_0
babel 2.9.1 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
beautifulsoup4 4.11.1 py39h06a4308_0
blas 1.0 mkl
bleach 4.1.0 pyhd3eb1b0_0
bottleneck 1.3.5 py39h7deecbd_0
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
brotlipy 0.7.0 py39hb9d737c_1004 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2023.5.7 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py39h74dc2b5_0
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge cryptography 37.0.4 py39hd97740a_0 conda-forge cudatoolkit 11.6.0 hecad31d_10 conda-forge cycler 0.11.0 pyhd3eb1b0_0
dbus 1.13.18 hb2f20db_0
debugpy 1.5.1 py39h295c915_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
dgl 0.9.1 py39_0 dglteam einops 0.6.1 pyhd8ed1ab_0 conda-forge entrypoints 0.4 py39h06a4308_0
executing 0.8.3 pyhd3eb1b0_0
expat 2.4.4 h295c915_0
ffmpeg 4.3 hf484d3e_0 pytorch filelock 3.9.0 py39h06a4308_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 hca18f0e_0 conda-forge glib 2.69.1 h4ff587b_1
glpk 5.0 h445213a_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gnutls 3.6.13 h85f3911_1 conda-forge gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 h28cd5cc_2
h5py 3.7.0 py39h737f45e_0
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge huggingface_hub 0.15.1 py_0 huggingface icu 58.2 he6710b0_3
idna 3.3 pyhd8ed1ab_0 conda-forge igraph 0.10.2 ha1f048c_0 conda-forge importlib-metadata 6.0.0 pyha770c72_0 conda-forge importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge ipykernel 6.9.1 py39h06a4308_0
ipython 8.4.0 py39h06a4308_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.5 pyhd3eb1b0_1
jedi 0.18.1 py39h06a4308_1
jinja2 3.0.3 pyhd3eb1b0_0
joblib 1.1.0 pyhd3eb1b0_0
jpeg 9e h166bdaf_2 conda-forge json5 0.9.6 pyhd3eb1b0_0
jsonschema 4.4.0 py39h06a4308_0
jupyter 1.0.0 py39h06a4308_8
jupyter_client 7.2.2 py39h06a4308_0
jupyter_console 6.4.3 pyhd3eb1b0_0
jupyter_core 4.10.0 py39h06a4308_0
jupyter_server 1.18.1 py39h06a4308_0
jupyterlab 3.4.4 py39h06a4308_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.12.0 py39h06a4308_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
kiwisolver 1.4.2 py39h295c915_0
lame 3.100 h7f98852_1001 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge leidenalg 0.9.1 py39h227be39_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 12_linux64_mkl conda-forge libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libcblas 3.9.0 12_linux64_mkl conda-forge libdeflate 1.13 h166bdaf_0 conda-forge libffi 3.3 he6710b0_2
libgcc-ng 12.1.0 h8d9b700_16 conda-forge libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 12_linux64_mkl conda-forge libllvm11 11.1.0 he0ac6c6_4 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libpng 1.6.37 h753d276_4 conda-forge libsodium 1.0.18 h7b6447c_0
libsqlite 3.39.2 h753d276_1 conda-forge libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge libtiff 4.4.0 h0e0dad5_3 conda-forge libuuid 1.0.3 h7f8727e_2
libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.9.14 h74e7548_0
libzlib 1.2.12 h166bdaf_2 conda-forge llvm-openmp 14.0.4 he0ac6c6_0 conda-forge llvmlite 0.39.1 py39h7d9a04d_0 conda-forge local-attention 1.8.6 pypi_0 pypi markupsafe 2.1.1 py39h7f8727e_0
matplotlib 3.5.1 py39h06a4308_1
matplotlib-base 3.5.1 py39ha18d171_1
matplotlib-inline 0.1.2 pyhd3eb1b0_2
metis 5.1.0 h58526e2_1006 conda-forge mistune 0.8.4 py39h27cfd23_1000
mkl 2021.4.0 h8d4b97c_729 conda-forge mkl-service 2.4.0 py39h7e14d7c_0 conda-forge mkl_fft 1.3.1 py39h0c7bc48_1 conda-forge mkl_random 1.2.2 py39hde0f152_0 conda-forge mpfr 4.1.0 h9202a9a_1 conda-forge munkres 1.1.4 py_0
natsort 8.2.0 pyhd8ed1ab_0 conda-forge nbclassic 0.3.5 pyhd3eb1b0_0
nbclient 0.5.13 py39h06a4308_0
nbconvert 6.4.4 py39h06a4308_0
nbformat 5.3.0 py39h06a4308_0
ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.5 py39h06a4308_0
nettle 3.6 he412f7d_0 conda-forge networkx 2.8.4 py39h06a4308_0
notebook 6.4.12 py39h06a4308_0
numba 0.56.4 py39h61ddf18_0 conda-forge numexpr 2.8.3 py39h807cd23_0
numpy 1.21.5 py39h6c91a56_3
numpy-base 1.21.5 py39ha15fc14_3
openh264 2.1.1 h780b84a_0 conda-forge openjpeg 2.5.0 h7d73246_1 conda-forge openssl 1.1.1u hd590300_0 conda-forge packaging 21.3 pyhd3eb1b0_0
pandas 1.4.3 py39h6a678d5_0
pandocfilters 1.5.0 pyhd3eb1b0_0
parso 0.8.3 pyhd3eb1b0_0
patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre 8.45 h295c915_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.2.0 py39hd5dbb17_2 conda-forge pip 22.2.2 pyhd8ed1ab_0 conda-forge plotly 5.9.0 py39h06a4308_0
prometheus_client 0.14.1 py39h06a4308_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
prompt_toolkit 3.0.20 hd3eb1b0_0
psutil 5.9.0 py39h5eee18b_0
pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.11.2 pyhd3eb1b0_0
pynndescent 0.5.8 pyh1a96a4e_0 conda-forge pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge pyparsing 3.0.4 pyhd3eb1b0_0
pyqt 5.9.2 py39h2531618_6
pyrsistent 0.18.0 py39heee7806_0
pysocks 1.7.1 py39hf3d152e_5 conda-forge python 3.9.12 h12debd9_1
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.15.1 pyhd3eb1b0_0
python-igraph 0.10.1 py39h000617a_1 conda-forge python_abi 3.9 2_cp39 conda-forge pytorch 1.12.1 py3.9_cuda11.6_cudnn8.3.2_0 pytorch pytorch-mutex 1.0 cuda pytorch pytz 2022.1 py39h06a4308_0
pyyaml 6.0 py39h5eee18b_1
pyzmq 23.2.0 py39h6a678d5_0
qt 5.9.7 h5867ecd_1
qtconsole 5.3.1 py39h06a4308_1
qtpy 2.0.1 pyhd3eb1b0_0
readline 8.1.2 h0f457ee_0 conda-forge regex 2022.7.9 py39h5eee18b_0
requests 2.28.1 pyhd8ed1ab_0 conda-forge scanpy 1.9.1 pyhd8ed1ab_0 conda-forge scikit-learn 0.23.2 pypi_0 pypi scipy 1.7.3 py39hc147768_0
scmer 0.1.0a4 pypi_0 pypi seaborn 0.12.1 py39h06a4308_0
send2trash 1.8.0 pyhd3eb1b0_1
session-info 1.0.0 pyhd8ed1ab_0 conda-forge setuptools 65.1.0 py39hf3d152e_0 conda-forge sip 4.19.13 py39h295c915_0
six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.2.0 py39h06a4308_1
soupsieve 2.3.1 pyhd3eb1b0_0
sqlite 3.39.2 h4ff8645_1 conda-forge stack_data 0.2.0 pyhd3eb1b0_0
statsmodels 0.13.5 py39h2ae25f5_2 conda-forge stdlib-list 0.8.0 pyhd8ed1ab_0 conda-forge suitesparse 5.10.1 h9e50725_1 conda-forge tbb 2021.5.0 h924138e_1 conda-forge tenacity 8.0.1 py39h06a4308_1
terminado 0.13.1 py39h06a4308_0
testpath 0.6.0 py39h06a4308_0
texttable 1.6.7 pyhd8ed1ab_0 conda-forge threadpoolctl 2.2.0 pyh0d69192_0
tk 8.6.12 h27826a3_0 conda-forge tokenizers 0.13.2 py39_0 huggingface torchaudio 0.12.1 py39_cu116 pytorch torchvision 0.13.1 py39_cu116 pytorch tornado 6.1 py39h27cfd23_0
tqdm 4.64.0 py39h06a4308_0
traitlets 5.1.1 pyhd3eb1b0_0
transformers 4.24.0 py39h06a4308_0
typing-extensions 4.5.0 py39h06a4308_0
typing_extensions 4.5.0 py39h06a4308_0
tzdata 2022c h191b570_0 conda-forge umap-learn 0.5.3 py39hf3d152e_0 conda-forge urllib3 1.26.11 pyhd8ed1ab_0 conda-forge wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py39h06a4308_1
websocket-client 0.58.0 py39h06a4308_4
wheel 0.37.1 pyhd8ed1ab_0 conda-forge widgetsnbextension 3.5.2 py39h06a4308_0
xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7b6447c_0
zeromq 4.3.4 h2531618_0
zipp 3.13.0 pyhd8ed1ab_0 conda-forge zlib 1.2.12 h166bdaf_2 conda-forge zstd 1.5.2 h6239696_4 conda-forge