trouble installing the package

snap-stanford / SATURN

MIT License

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File ".../anaconda3/envs/SATURN/lib/python3.9/site-packages/lightning/fabric/utilities/types.py", line 37, in <module> torch.UntypedStorage if _TORCH_GREATER_EQUAL_1_13 else torch._UntypedStorage # type: ignore[valid-type] AttributeError: module 'torch' has no attribute '_UntypedStorage'

I think I might have got it working by playing around with package versions, until there is some official fix you can try these.

requirements.txt

``` absl-py==2.1.0 aiobotocore==2.13.1 aiohttp==3.9.5 aioitertools==0.11.0 aiosignal==1.3.1 anndata==0.10.8 annotated-types==0.7.0 antlr4-python3-runtime==4.9.3 anyio==4.4.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 array_api_compat==1.7.1 arrow==1.3.0 asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work async-lru==2.0.4 async-timeout==4.0.3 attrs==23.2.0 Babel==2.15.0 backoff==2.2.1 beautifulsoup4==4.12.3 biopython==1.84 bleach==6.1.0 blessed==1.20.0 boto3==1.34.131 botocore==1.34.131 certifi==2024.6.2 cffi==1.16.0 charset-normalizer==3.3.2 chex==0.1.7 click==8.1.7 comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1710320294760/work contextlib2==21.6.0 contourpy==1.2.1 croniter==1.3.15 cycler==0.12.1 daal==2024.5.0 daal4py==2024.5.0 dateutils==0.6.12 debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1719378673901/work decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work deepdiff==7.0.1 defusedxml==0.7.1 dm-tree==0.1.8 dnspython==2.6.1 docrep==0.3.2 docstring_parser==0.16 editor==1.6.6 email_validator==2.2.0 ensembl-rest==0.3.4 et-xmlfile==1.1.0 etils==1.5.2 exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1704921103267/work executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work fair-esm==2.0.0 faiss-gpu==1.7.2 fastapi==0.88.0 fastapi-cli==0.0.4 fastjsonschema==2.20.0 filelock==3.15.4 fire==0.6.0 flax==0.8.5 fonttools==4.53.0 fqdn==1.5.1 frozenlist==1.4.1 fsspec==2023.12.2 future==1.0.0 get-annotations==0.1.2 grpcio==1.64.1 h11==0.14.0 h5py==3.11.0 httpcore==1.0.5 httptools==0.6.1 httpx==0.27.0 hydra-core==1.3.2 idna==3.7 igraph==0.11.5 importlib_metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1719361860083/work importlib_resources==6.4.0 inquirer==3.3.0 intervaltree==3.1.0 ipdb==0.13.13 ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1717717528849/work ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1701831663892/work ipywidgets==8.1.3 isoduration==20.11.0 itsdangerous==2.2.0 jax==0.4.30 jaxlib==0.4.30 jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work Jinja2==3.1.4 jmespath==1.0.1 joblib==1.4.2 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.22.0 jsonschema-specifications==2023.12.1 jupyter-events==0.10.0 jupyter-lsp==2.2.5 jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1716472197302/work jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1710257447442/work jupyter_server==2.14.1 jupyter_server_terminals==0.5.3 jupyterlab==4.2.3 jupyterlab_pygments==0.3.0 jupyterlab_server==2.27.2 jupyterlab_widgets==3.0.11 kiwisolver==1.4.5 legacy-api-wrap==1.4 lightning-cloud==0.5.70 lightning-lite==1.8.6 lightning-utilities==0.11.3.post0 llvmlite==0.43.0 louvain==0.8.2 Markdown==3.6 markdown-it-py==3.0.0 MarkupSafe==2.1.5 matplotlib==3.9.0 matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1713250518406/work mdurl==0.1.2 mistune==3.0.2 ml-dtypes==0.4.0 ml_collections==0.1.1 mpmath==1.3.0 msgpack==1.0.8 mudata==0.2.4 multidict==6.0.5 multipledispatch==1.0.0 mypy-extensions==1.0.0 natsort==8.4.0 nbclient==0.10.0 nbconvert==7.16.4 nbformat==5.10.4 nest_asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1705850609492/work networkx==3.2.1 notebook==7.2.1 notebook_shim==0.2.4 numba==0.60.0 numpy==1.26.4 numpyro==0.15.0 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 nvidia-cuda-runtime-cu12==12.1.105 nvidia-cudnn-cu12==8.9.2.26 nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 nvidia-nccl-cu12==2.20.5 nvidia-nvjitlink-cu12==12.5.40 nvidia-nvtx-cu12==12.1.105 omegaconf==2.3.0 openpyxl==3.1.5 opt-einsum==3.3.0 optax==0.2.1 orbax-checkpoint==0.5.20 ordered-set==4.1.0 orjson==3.10.6 overrides==7.7.0 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work pandas==1.5.0 pandocfilters==1.5.1 parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1712320355065/work patsy==0.5.6 pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1706113125309/work pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work pillow==10.3.0 platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1715777629804/work plotly==5.22.0 prometheus_client==0.20.0 prompt_toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1718047967974/work protobuf==3.20.1 psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1719274564771/work ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work pycparser==2.22 pydantic==1.10.17 pydantic_core==2.4.0 pyDeprecate==0.3.0 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1714846767233/work PyJWT==2.8.0 pynndescent==0.5.13 pyparsing==3.1.2 pyro-api==0.1.2 pyro-ppl==1.8.0 python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work python-dotenv==1.0.1 python-json-logger==2.0.7 python-multipart==0.0.9 pytorch-lightning==1.3.8 pytz==2024.1 PyYAML==5.4.1 pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1715024408309/work readchar==4.1.0 record-keeper==0.9.32 referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 rich==13.7.1 rpds-py==0.18.1 runs==1.2.2 s3fs==2023.12.2 s3transfer==0.10.2 scanpy==1.10.2 scikit-learn==1.5.0 scikit-learn-intelex==2024.5.0 scikit-misc==0.3.1 scipy==1.13.1 scvi-tools==0.14.0 seaborn==0.13.2 Send2Trash==1.8.3 session_info==1.0.0 shellingham==1.5.4 simplejson==3.19.2 six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work sniffio==1.3.1 sortedcontainers==2.4.0 soupsieve==2.5 sparse==0.15.4 stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work starlette==0.22.0 starsessions==1.3.0 statsmodels==0.14.2 stdlib-list==0.10.0 sympy==1.12.1 tbb==2021.13.0 tenacity==8.4.2 tensorboard==2.17.0 tensorboard-data-server==0.7.2 tensorstore==0.1.63 termcolor==2.4.0 terminado==0.18.1 texttable==1.7.0 threadpoolctl==3.5.0 tinycss2==1.3.0 tomli==2.0.1 toolz==0.12.1 torch==1.10.2+cu113 torchmetrics==0.6.0 torchvision==0.11.3 tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1717722887379/work tqdm==4.66.4 traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1713535121073/work triton==2.3.1 typed-argument-parser==1.10.0 typer==0.12.3 types-python-dateutil==2.9.0.20240316 typing-inspect==0.9.0 typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1717802530399/work tzdata==2024.1 ujson==5.10.0 umap-learn==0.5.6 uri-template==1.3.0 urllib3==1.26.19 uvicorn==0.30.1 uvloop==0.19.0 watchfiles==0.22.0 wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1704731205417/work webcolors==24.6.0 webencodings==0.5.1 websocket-client==1.8.0 websockets==11.0.3 Werkzeug==3.0.3 widgetsnbextension==4.0.11 wrapt==1.16.0 xarray==2024.3.0 xmod==1.8.1 yarl==1.9.4 zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1718013267051/work ```

I think I might have got it working by playing around with package versions, until there is some official fix you can try these.

requirements.txt

absl-py==2.1.0
aiobotocore==2.13.1
aiohttp==3.9.5
aioitertools==0.11.0
aiosignal==1.3.1
anndata==0.10.8
annotated-types==0.7.0
antlr4-python3-runtime==4.9.3
anyio==4.4.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
array_api_compat==1.7.1
arrow==1.3.0
asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work
async-lru==2.0.4
async-timeout==4.0.3
attrs==23.2.0
Babel==2.15.0
backoff==2.2.1
beautifulsoup4==4.12.3
biopython==1.84
bleach==6.1.0
blessed==1.20.0
boto3==1.34.131
botocore==1.34.131
certifi==2024.6.2
cffi==1.16.0
charset-normalizer==3.3.2
chex==0.1.7
click==8.1.7
comm @ file:///home/conda/feedstock_root/build_artifacts/comm_1710320294760/work
contextlib2==21.6.0
contourpy==1.2.1
croniter==1.3.15
cycler==0.12.1
daal==2024.5.0
daal4py==2024.5.0
dateutils==0.6.12
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1719378673901/work
decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work
deepdiff==7.0.1
defusedxml==0.7.1
dm-tree==0.1.8
dnspython==2.6.1
docrep==0.3.2
docstring_parser==0.16
editor==1.6.6
email_validator==2.2.0
ensembl-rest==0.3.4
et-xmlfile==1.1.0
etils==1.5.2
exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1704921103267/work
executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work
fair-esm==2.0.0
faiss-gpu==1.7.2
fastapi==0.88.0
fastapi-cli==0.0.4
fastjsonschema==2.20.0
filelock==3.15.4
fire==0.6.0
flax==0.8.5
fonttools==4.53.0
fqdn==1.5.1
frozenlist==1.4.1
fsspec==2023.12.2
future==1.0.0
get-annotations==0.1.2
grpcio==1.64.1
h11==0.14.0
h5py==3.11.0
httpcore==1.0.5
httptools==0.6.1
httpx==0.27.0
hydra-core==1.3.2
idna==3.7
igraph==0.11.5
importlib_metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1719361860083/work
importlib_resources==6.4.0
inquirer==3.3.0
intervaltree==3.1.0
ipdb==0.13.13
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1717717528849/work
ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1701831663892/work
ipywidgets==8.1.3
isoduration==20.11.0
itsdangerous==2.2.0
jax==0.4.30
jaxlib==0.4.30
jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work
Jinja2==3.1.4
jmespath==1.0.1
joblib==1.4.2
json5==0.9.25
jsonpointer==3.0.0
jsonschema==4.22.0
jsonschema-specifications==2023.12.1
jupyter-events==0.10.0
jupyter-lsp==2.2.5
jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1716472197302/work
jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1710257447442/work
jupyter_server==2.14.1
jupyter_server_terminals==0.5.3
jupyterlab==4.2.3
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.2
jupyterlab_widgets==3.0.11
kiwisolver==1.4.5
legacy-api-wrap==1.4
lightning-cloud==0.5.70
lightning-lite==1.8.6
lightning-utilities==0.11.3.post0
llvmlite==0.43.0
louvain==0.8.2
Markdown==3.6
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.9.0
matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1713250518406/work
mdurl==0.1.2
mistune==3.0.2
ml-dtypes==0.4.0
ml_collections==0.1.1
mpmath==1.3.0
msgpack==1.0.8
mudata==0.2.4
multidict==6.0.5
multipledispatch==1.0.0
mypy-extensions==1.0.0
natsort==8.4.0
nbclient==0.10.0
nbconvert==7.16.4
nbformat==5.10.4
nest_asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1705850609492/work
networkx==3.2.1
notebook==7.2.1
notebook_shim==0.2.4
numba==0.60.0
numpy==1.26.4
numpyro==0.15.0
nvidia-cublas-cu12==12.1.3.1
nvidia-cuda-cupti-cu12==12.1.105
nvidia-cuda-nvrtc-cu12==12.1.105
nvidia-cuda-runtime-cu12==12.1.105
nvidia-cudnn-cu12==8.9.2.26
nvidia-cufft-cu12==11.0.2.54
nvidia-curand-cu12==10.3.2.106
nvidia-cusolver-cu12==11.4.5.107
nvidia-cusparse-cu12==12.1.0.106
nvidia-nccl-cu12==2.20.5
nvidia-nvjitlink-cu12==12.5.40
nvidia-nvtx-cu12==12.1.105
omegaconf==2.3.0
openpyxl==3.1.5
opt-einsum==3.3.0
optax==0.2.1
orbax-checkpoint==0.5.20
ordered-set==4.1.0
orjson==3.10.6
overrides==7.7.0
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work
pandas==1.5.0
pandocfilters==1.5.1
parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1712320355065/work
patsy==0.5.6
pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1706113125309/work
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
pillow==10.3.0
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1715777629804/work
plotly==5.22.0
prometheus_client==0.20.0
prompt_toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1718047967974/work
protobuf==3.20.1
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1719274564771/work
ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work
pycparser==2.22
pydantic==1.10.17
pydantic_core==2.4.0
pyDeprecate==0.3.0
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1714846767233/work
PyJWT==2.8.0
pynndescent==0.5.13
pyparsing==3.1.2
pyro-api==0.1.2
pyro-ppl==1.8.0
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work
python-dotenv==1.0.1
python-json-logger==2.0.7
python-multipart==0.0.9
pytorch-lightning==1.3.8
pytz==2024.1
PyYAML==5.4.1
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1715024408309/work
readchar==4.1.0
record-keeper==0.9.32
referencing==0.35.1
requests==2.32.3
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rich==13.7.1
rpds-py==0.18.1
runs==1.2.2
s3fs==2023.12.2
s3transfer==0.10.2
scanpy==1.10.2
scikit-learn==1.5.0
scikit-learn-intelex==2024.5.0
scikit-misc==0.3.1
scipy==1.13.1
scvi-tools==0.14.0
seaborn==0.13.2
Send2Trash==1.8.3
session_info==1.0.0
shellingham==1.5.4
simplejson==3.19.2
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
sniffio==1.3.1
sortedcontainers==2.4.0
soupsieve==2.5
sparse==0.15.4
stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work
starlette==0.22.0
starsessions==1.3.0
statsmodels==0.14.2
stdlib-list==0.10.0
sympy==1.12.1
tbb==2021.13.0
tenacity==8.4.2
tensorboard==2.17.0
tensorboard-data-server==0.7.2
tensorstore==0.1.63
termcolor==2.4.0
terminado==0.18.1
texttable==1.7.0
threadpoolctl==3.5.0
tinycss2==1.3.0
tomli==2.0.1
toolz==0.12.1
torch==1.10.2+cu113
torchmetrics==0.6.0
torchvision==0.11.3
tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1717722887379/work
tqdm==4.66.4
traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1713535121073/work
triton==2.3.1
typed-argument-parser==1.10.0
typer==0.12.3
types-python-dateutil==2.9.0.20240316
typing-inspect==0.9.0
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1717802530399/work
tzdata==2024.1
ujson==5.10.0
umap-learn==0.5.6
uri-template==1.3.0
urllib3==1.26.19
uvicorn==0.30.1
uvloop==0.19.0
watchfiles==0.22.0
wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1704731205417/work
webcolors==24.6.0
webencodings==0.5.1
websocket-client==1.8.0
websockets==11.0.3
Werkzeug==3.0.3
widgetsnbextension==4.0.11
wrapt==1.16.0
xarray==2024.3.0
xmod==1.8.1
yarl==1.9.4
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1718013267051/work

Hi @jlr13 ,

Do you install these packages in a python 3.8 environment? Also I am curious what versions are you using for those self-built libraries. I am having trouble installing packages in this file.

Thanks, Wei

snap-stanford / SATURN

trouble installing the package #63