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frankligy / scTriangulate

scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
MIT License
35 stars 5 forks source link

OSError [Errno 16] in installation #4

Closed KANG-BIOINFO closed 3 years ago

KANG-BIOINFO commented 3 years ago

Hi, here is an error I met during installation using pip in the Linux system:

[jinmr2@bmiclusterp3 time_samplegroup_celltype_KO]$ /data/aronow/Kang/py_envir/aipy/bin/python3.7 -m pip install sctriangulate
Collecting sctriangulate
  Downloading sctriangulate-0.9.1-py3-none-any.whl (125 kB)
     |████████████████████████████████| 125 kB 4.2 MB/s 
Collecting yattag
  Downloading yattag-1.14.0.tar.gz (26 kB)
Collecting gseapy==0.10.4
  Downloading gseapy-0.10.4-py3-none-any.whl (525 kB)
     |████████████████████████████████| 525 kB 13.2 MB/s 
Requirement already satisfied: leidenalg in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from sctriangulate) (0.8.4)
Collecting mygene==3.2.2
  Downloading mygene-3.2.2-py2.py3-none-any.whl (5.4 kB)
Collecting pandas==1.1.5
  Using cached pandas-1.1.5-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB)
Requirement already satisfied: scanpy==1.7.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from sctriangulate) (1.7.2)
Requirement already satisfied: scrublet==0.2.3 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from sctriangulate) (0.2.3)
Collecting anytree
  Downloading anytree-2.8.0-py2.py3-none-any.whl (41 kB)
     |████████████████████████████████| 41 kB 240 kB/s 
Collecting numpy==1.19.5
  Downloading numpy-1.19.5-cp37-cp37m-manylinux2010_x86_64.whl (14.8 MB)
     |████████████████████████████████| 14.8 MB 40.3 MB/s 
Requirement already satisfied: scipy in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gseapy==0.10.4->sctriangulate) (1.6.3)
Requirement already satisfied: bioservices in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gseapy==0.10.4->sctriangulate) (1.7.12)
Requirement already satisfied: requests in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gseapy==0.10.4->sctriangulate) (2.25.1)
Requirement already satisfied: matplotlib in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gseapy==0.10.4->sctriangulate) (3.4.2)
Requirement already satisfied: joblib in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gseapy==0.10.4->sctriangulate) (1.0.1)
Collecting biothings-client>=0.2.6
  Downloading biothings_client-0.2.6-py2.py3-none-any.whl (37 kB)
Requirement already satisfied: pytz>=2017.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from pandas==1.1.5->sctriangulate) (2021.1)
Requirement already satisfied: python-dateutil>=2.7.3 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from pandas==1.1.5->sctriangulate) (2.8.1)
Requirement already satisfied: umap-learn>=0.3.10 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.5.1)
Requirement already satisfied: networkx>=2.3 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (2.5.1)
Requirement already satisfied: natsort in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (7.1.1)
Requirement already satisfied: packaging in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (20.9)
Requirement already satisfied: legacy-api-wrap in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (1.2)
Requirement already satisfied: sinfo in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.3.4)
Requirement already satisfied: h5py>=2.10.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (2.10.0)
Requirement already satisfied: tables in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (3.6.1)
Requirement already satisfied: patsy in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.5.1)
Requirement already satisfied: tqdm in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (4.60.0)
Requirement already satisfied: statsmodels>=0.10.0rc2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.12.2)
Requirement already satisfied: seaborn in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.11.1)
Requirement already satisfied: scikit-learn>=0.21.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.24.2)
Requirement already satisfied: anndata>=0.7.4 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.7.6)
Requirement already satisfied: numba>=0.41.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (0.53.1)
Requirement already satisfied: importlib-metadata>=0.7 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scanpy==1.7.2->sctriangulate) (1.7.0)
Requirement already satisfied: annoy in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scrublet==0.2.3->sctriangulate) (1.17.0)
Requirement already satisfied: scikit-image in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scrublet==0.2.3->sctriangulate) (0.18.3)
Requirement already satisfied: cython in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scrublet==0.2.3->sctriangulate) (0.29.24)
Requirement already satisfied: xlrd<2.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from anndata>=0.7.4->scanpy==1.7.2->sctriangulate) (1.2.0)
Requirement already satisfied: six in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from h5py>=2.10.0->scanpy==1.7.2->sctriangulate) (1.16.0)
Requirement already satisfied: zipp>=0.5 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from importlib-metadata>=0.7->scanpy==1.7.2->sctriangulate) (3.4.1)
Requirement already satisfied: cycler>=0.10 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from matplotlib->gseapy==0.10.4->sctriangulate) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from matplotlib->gseapy==0.10.4->sctriangulate) (1.3.1)
Requirement already satisfied: pyparsing>=2.2.1 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from matplotlib->gseapy==0.10.4->sctriangulate) (2.4.7)
Requirement already satisfied: pillow>=6.2.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from matplotlib->gseapy==0.10.4->sctriangulate) (8.2.0)
Requirement already satisfied: decorator<5,>=4.3 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from networkx>=2.3->scanpy==1.7.2->sctriangulate) (4.4.2)
Requirement already satisfied: llvmlite<0.37,>=0.36.0rc1 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from numba>=0.41.0->scanpy==1.7.2->sctriangulate) (0.36.0)
Requirement already satisfied: setuptools in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from numba>=0.41.0->scanpy==1.7.2->sctriangulate) (52.0.0.post20210125)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests->gseapy==0.10.4->sctriangulate) (1.26.4)
Requirement already satisfied: idna<3,>=2.5 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests->gseapy==0.10.4->sctriangulate) (2.10)
Requirement already satisfied: chardet<5,>=3.0.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests->gseapy==0.10.4->sctriangulate) (4.0.0)
Requirement already satisfied: certifi>=2017.4.17 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests->gseapy==0.10.4->sctriangulate) (2020.12.5)
Requirement already satisfied: threadpoolctl>=2.0.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scikit-learn>=0.21.2->scanpy==1.7.2->sctriangulate) (2.1.0)
Requirement already satisfied: pynndescent>=0.5 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from umap-learn>=0.3.10->scanpy==1.7.2->sctriangulate) (0.5.2)
Requirement already satisfied: lxml in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (4.6.3)
Requirement already satisfied: beautifulsoup4 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (4.10.0)
Requirement already satisfied: requests-cache in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (0.8.0)
Requirement already satisfied: appdirs in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (1.4.4)
Requirement already satisfied: suds-jurko in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (0.6)
Requirement already satisfied: grequests in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (0.6.0)
Requirement already satisfied: easydev>=0.9.36 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (0.12.0)
Requirement already satisfied: colorlog in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (6.4.1)
Requirement already satisfied: xmltodict in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (0.12.0)
Requirement already satisfied: wrapt in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from bioservices->gseapy==0.10.4->sctriangulate) (1.12.1)
Requirement already satisfied: pexpect in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from easydev>=0.9.36->bioservices->gseapy==0.10.4->sctriangulate) (4.8.0)
Requirement already satisfied: colorama in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from easydev>=0.9.36->bioservices->gseapy==0.10.4->sctriangulate) (0.4.4)
Requirement already satisfied: soupsieve>1.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from beautifulsoup4->bioservices->gseapy==0.10.4->sctriangulate) (2.2.1)
Requirement already satisfied: gevent in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from grequests->bioservices->gseapy==0.10.4->sctriangulate) (21.8.0)
Requirement already satisfied: greenlet<2.0,>=1.1.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gevent->grequests->bioservices->gseapy==0.10.4->sctriangulate) (1.1.1)
Requirement already satisfied: zope.event in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gevent->grequests->bioservices->gseapy==0.10.4->sctriangulate) (4.5.0)
Requirement already satisfied: zope.interface in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from gevent->grequests->bioservices->gseapy==0.10.4->sctriangulate) (5.4.0)
Requirement already satisfied: get-version>=2.0.4 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from legacy-api-wrap->scanpy==1.7.2->sctriangulate) (2.2)
Requirement already satisfied: python-igraph>=0.9.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from leidenalg->sctriangulate) (0.9.6)
Requirement already satisfied: texttable>=1.6.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from python-igraph>=0.9.0->leidenalg->sctriangulate) (1.6.3)
Requirement already satisfied: ptyprocess>=0.5 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from pexpect->easydev>=0.9.36->bioservices->gseapy==0.10.4->sctriangulate) (0.7.0)
Requirement already satisfied: attrs<22.0,>=21.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests-cache->bioservices->gseapy==0.10.4->sctriangulate) (21.2.0)
Requirement already satisfied: url-normalize<2.0,>=1.4 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests-cache->bioservices->gseapy==0.10.4->sctriangulate) (1.4.3)
Requirement already satisfied: cattrs<2.0,>=1.8 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from requests-cache->bioservices->gseapy==0.10.4->sctriangulate) (1.8.0)
Requirement already satisfied: PyWavelets>=1.1.1 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scikit-image->scrublet==0.2.3->sctriangulate) (1.1.1)
Requirement already satisfied: tifffile>=2019.7.26 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scikit-image->scrublet==0.2.3->sctriangulate) (2021.8.30)
Requirement already satisfied: imageio>=2.3.0 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from scikit-image->scrublet==0.2.3->sctriangulate) (2.9.0)
Requirement already satisfied: stdlib-list in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from sinfo->scanpy==1.7.2->sctriangulate) (0.8.0)
Requirement already satisfied: numexpr>=2.6.2 in /data/aronow/Kang/py_envir/aipy/lib/python3.7/site-packages (from tables->scanpy==1.7.2->sctriangulate) (2.7.3)
Building wheels for collected packages: yattag
  Building wheel for yattag (setup.py) ... done
  Created wheel for yattag: filename=yattag-1.14.0-py3-none-any.whl size=15659 sha256=fd7971e404bffb9c41d0cd2c5eb96f5e07859aba15fd3bc764d459609034da16
  Stored in directory: /users/jinmr2/.cache/pip/wheels/4d/32/61/f205e276a280e24c3fca996bd956781b2a0fbad498161e53f4
Successfully built yattag
Installing collected packages: numpy, pandas, biothings-client, yattag, mygene, gseapy, anytree, sctriangulate
  Attempting uninstall: numpy
    Found existing installation: numpy 1.18.5
    Uninstalling numpy-1.18.5:
      Successfully uninstalled numpy-1.18.5
ERROR: Could not install packages due to an OSError: [Errno 16] Device or resource busy: '.nfs00000005b0635d6b00005bf3'

My environment is listed as below:

/data/aronow/Kang/py_envir/aipy/bin/python3.7 -m pip freeze
absl-py==0.12.0
adjustText==0.7.3
aiohttp==3.7.4.post0
anndata==0.7.6
annoy==1.17.0
appdirs==1.4.4
argon2-cffi==20.1.0
arviz==0.11.2
astunparse==1.6.3
async-generator==1.10
async-timeout==3.0.1
attrs==21.2.0
backcall==0.2.0
beautifulsoup4==4.10.0
bioinfokit==2.0.6
biopython==1.79
bioservices==1.7.12
bleach==3.3.0
cachetools==4.2.2
cattrs==1.8.0
certifi==2020.12.5
cffi==1.14.5
cftime==1.4.1
chardet==4.0.0
click==8.0.1
cloudpickle==1.3.0
colorama==0.4.4
colorlog==6.4.1
commonmark==0.9.1
compert @ git+https://github.com/facebookresearch/CPA.git@382ff641c588820a453d801e5d0e5bb56642f282
cycler==0.10.0
Cython==0.29.24
decorator==4.4.2
defusedxml==0.7.1
dm-tree==0.1.6
doubletdetection==3.0
easydev==0.12.0
entrypoints==0.3
et-xmlfile==1.1.0
fsspec==2021.5.0
future==0.18.2
gast==0.3.3
get-version==2.2
gevent==21.8.0
google-auth==1.30.0
google-auth-oauthlib==0.4.4
google-pasta==0.2.0
greenlet==1.1.1
grequests==0.6.0
grpcio==1.37.1
gseapy==0.10.5
h5py==2.10.0
harmonypy==0.0.5
idna==2.10
imageio==2.9.0
importlib-metadata==1.7.0
iniconfig==1.1.1
ipykernel==5.5.5
ipython==7.23.1
ipython-genutils==0.2.0
ipywidgets==7.6.3
jedi==0.18.0
Jinja2==3.0.0
joblib==1.0.1
jsonschema==3.2.0
jupyter-client==6.1.12
jupyter-core==4.7.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.0
kaleido==0.2.1
Keras-Preprocessing==1.1.2
kiwisolver==1.3.1
legacy-api-wrap==1.2
leidenalg==0.8.4
llvmlite==0.36.0
loompy==3.0.6
louvain==0.7.0
lxml==4.6.3
Markdown==3.3.4
MarkupSafe==2.0.0
matplotlib==3.4.2
matplotlib-inline==0.1.2
matplotlib-venn==0.11.6
milopy @ file:///data/aronow/Kang/single_cell_projects/10X-Pak/integration/patient_derived_engineered/v2_filtered/DA_analysis/milopy
mistune==0.8.4
multidict==5.1.0
natsort==7.1.1
nbclient==0.5.3
nbconvert==6.0.7
nbformat==5.1.3
nest-asyncio==1.5.1
netCDF4==1.5.6
networkx==2.5.1
notebook==6.4.0
numba==0.53.1
numexpr==2.7.3
numpy==1.19.5
numpy-groupies==0.9.14
oauthlib==3.1.0
openpyxl==3.0.7
opt-einsum==3.3.0
packaging==20.9
palettable==3.3.0
pandas==1.2.4
pandocfilters==1.4.3
parso==0.8.2
patsy==0.5.1
pexpect==4.8.0
PhenoGraph==1.5.7
pickleshare==0.7.5
Pillow==8.2.0
plotly==5.3.1
pluggy==0.13.1
prometheus-client==0.10.1
prompt-toolkit==3.0.18
protobuf==3.17.0
psutil==5.8.0
ptyprocess==0.7.0
py==1.10.0
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycparser==2.20
Pygments==2.9.0
pynndescent==0.5.2
pyparsing==2.4.7
pyro-api==0.1.2
pyro-ppl==1.6.0
pyrsistent==0.17.3
pysam==0.16.0.1
pytest==6.2.4
python-dateutil==2.8.1
python-igraph==0.9.6
pytorch-lightning==1.2.10
pytz==2021.1
PyWavelets==1.1.1
PyYAML==5.3.1
pyzmq==22.0.3
requests==2.25.1
requests-cache==0.8.0
requests-oauthlib==1.3.0
rich==10.2.0
rpy2==3.4.5
rsa==4.7.2
scanpy==1.7.2
scCODA==0.1.2.post1
scgen==2.0.0
scikit-image==0.18.3
scikit-learn==0.24.2
scikit-misc==0.1.4
scipy==1.6.3
scrublet==0.2.3
scvi-tools==0.10.1
seaborn==0.11.1
Send2Trash==1.5.0
shap==0.39.0
simplegeneric==0.8.1
sinfo==0.3.4
six==1.16.0
sklearn==0.0
slicer==0.0.7
soupsieve==2.2.1
statsmodels==0.12.2
stdlib-list==0.8.0
submitit==1.3.3
suds-jurko==0.6
tables==3.6.1
tabulate==0.8.9
tenacity==8.0.1
tensorboard==2.4.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
tensorflow==2.3.2
tensorflow-estimator==2.3.0
tensorflow-probability==0.11.0
termcolor==1.1.0
terminado==0.9.5
testpath==0.5.0
texttable==1.6.3
textwrap3==0.9.2
threadpoolctl==2.1.0
tifffile==2021.8.30
toml==0.10.2
torch==1.8.1+cpu
torchaudio==0.8.1
torchmetrics==0.2.0
torchvision==0.9.1+cpu
tornado==6.1
tqdm==4.60.0
traitlets==5.0.5
typing-extensions==3.10.0.0
tzlocal==2.1
umap-learn==0.5.1
url-normalize==1.4.3
urllib3==1.26.4
velocyto==0.17.17
wcwidth==0.2.5
webencodings==0.5.1
Werkzeug==2.0.0
widgetsnbextension==3.5.1
wrapt==1.12.1
xarray==0.18.0
xgboost==1.4.2
xlrd==1.2.0
xmltodict==0.12.0
yarl==1.6.3
zipp==3.4.1
zope.event==4.5.0
zope.interface==5.4.0
frankligy commented 3 years ago

This is a system error, please see (https://stackoverflow.com/questions/55693629/getting-oserror-errno-16-device-or-resource-busy-when-using-tf-keras-model).

I would recommend first make sure no other interactive session or other things are running on the same time on the cluster.

KANG-BIOINFO commented 3 years ago

Now it works.

frankligy commented 3 years ago

Great!