nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS"

[XscapeCn]

Hello, after I install Camoco, I run $camocoand I get such a error:

Error.  nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)Traceback (most recent call last):
  File "/data1/home/songxu/software/anaconda3/envs/work/bin/camoco", line 4, in <module>
    __import__('pkg_resources').run_script('camoco==0.6.4', 'camoco')
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/pkg_resources/__init__.py", line 665, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1463, in run_script
    exec(code, namespace, namespace)
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/camoco-0.6.4-py3.8-linux-x86_64.egg/EGG-INFO/scripts/camoco", line 17, in <module>
    import camoco as co
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/camoco-0.6.4-py3.8-linux-x86_64.egg/camoco/__init__.py", line 73, in <module>
    from .COB import COB
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/camoco-0.6.4-py3.8-linux-x86_64.egg/camoco/COB.py", line 41, in <module>
    from odo import odo
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/odo-0.5.0-py3.8.egg/odo/__init__.py", line 39, in <module>
    from .backends import sql
  File "/data1/home/songxu/software/anaconda3/envs/work/lib/python3.8/site-packages/odo-0.5.0-py3.8.egg/odo/backends/sql.py", line 304, in <module>
    @discover.register(sa.engine.RowProxy)
AttributeError: module 'sqlalchemy.engine' has no attribute 'RowProxy'

Could you give me some advice?
Thank you!

[schae234]

Hi @XscapeCn thanks for filing an issue, sorry for the problems. Can you post the output from pip freeze? Camoco is at a weird stage right now, several of the core packages we initially used for analysis are totally abandoned. I'm in the process of a total re-write but I am not able to dedicate as much time to Camoco development as I used to. However, I'd like to help you if I am able.

The package giving you problems here is odo which hasn't been updated for years. In terms of your specific error, my guess is that odo needs an older version of sqlalchemy to work properly. If you provide the package versions from pip freeze we may be able to figure out of an older library would work. Another option is to look at older sqlalchemy releases by date and try to target a release from ~2017.

[XscapeCn]

Thank you for your reply! The result of $pip freeze is below.

absl-py==0.9.0
apsw==3.27.2.post1
astunparse==1.6.3
asyncssh==2.5.0
attrs==19.3.0
backcall==0.2.0
backoff==1.10.0
bcolz==1.2.1
blaze==0.10.1
bleach==3.1.5
blinker==1.4
boto3==1.16.51
botocore==1.19.51
brotlipy==0.7.0
cachetools==4.1.0
camoco==0.6.4
certifi==2020.6.20
cffi==1.14.4
chardet==3.0.4
click==7.1.2
cryptography==2.9.2
cycler==0.10.0
Cython==0.29.21
dask==2.30.0
dataclasses==0.6
datashape==0.5.2
decorator==4.4.2
defusedxml==0.6.0
Deprecated==1.2.10
entrypoints==0.3
fa2==0.3.5
fastcluster==1.1.26
Flask==1.0.3
Flask-Cors==3.0.10
fsspec==0.8.4
future==0.18.2
fuzzywuzzy==0.18.0
gast==0.3.3
gcloud==0.18.3
google-api-core==1.24.1
google-auth==1.21.1
google-auth-oauthlib==0.4.1
google-cloud==0.34.0
google-cloud-core==1.5.0
google-cloud-storage==1.35.0
google-crc32c==1.1.0
google-pasta==0.2.0
google-resumable-media==1.2.0
googleapis-common-protos==1.52.0
greenlet==1.0a1
grpcio==1.27.2
h5py @ file:///tmp/build/80754af9/h5py_1593454122442/work
httplib2==0.18.1
idna @ file:///tmp/build/80754af9/idna_1593446292537/work
igraph==0.1.11
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1593446406207/work
iniconfig==1.1.1
ipykernel @ file:///tmp/build/80754af9/ipykernel_1594753368510/work/dist/ipykernel-5.3.2-py3-none-any.whl
ipython @ file:///tmp/build/80754af9/ipython_1593447377063/work
ipython-genutils==0.2.0
ipywidgets==7.5.1
itsdangerous==2.0.0a1
jedi @ file:///tmp/build/80754af9/jedi_1592841866100/work
Jinja2==2.11.2
jmespath==0.10.0
joblib==1.0.0
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1594826976318/work
jupyter-console==6.2.0
jupyter-core==4.6.3
jwcrypto==0.8
Keras @ file:///tmp/build/80754af9/keras_split_1593112142734/work
Keras-Preprocessing==1.1.0
kiwisolver==1.3.1
locket==0.2.0
Markdown==3.1.1
markov-clustering==0.0.6.dev0
MarkupSafe==1.1.1
matplotlib==3.3.3
minus80==1.0.0
mistune==0.8.4
mkl-fft==1.1.0
mkl-random==1.1.1
mkl-service==2.3.0
mpmath==1.1.0
multipledispatch==0.6.0
nbconvert==5.6.1
nbformat==5.0.7
networkx==1.11
notebook==6.0.3
numexpr==2.7.2
numpy==1.18.5
oauth2client==4.1.3
oauthlib==3.1.0
odo==0.5.0
opt-einsum==3.1.0
packaging==20.4
pandas==0.23.4
pandas-plink==2.2.4
pandocfilters==1.4.2
parso==0.7.0
partd==1.1.0
patsy==0.5.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.0.1
pluggy==0.13.1
powerlaw==1.4.6
prometheus-client==0.8.0
prompt-toolkit==3.0.5
protobuf==3.12.3
psutil==5.8.0
ptyprocess==0.6.0
py==1.9.0
pyarrow==2.0.0
pyasn1==0.4.8
pyasn1-modules==0.2.7
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pycryptodome==3.9.9
Pygments==2.6.1
PyJWT==1.7.1
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1594392929924/work
pyparsing==2.4.7
Pyrebase4==4.4.3
pyrsistent==0.16.0
PySocks==1.7.1
pytest==6.1.2
python-dateutil==2.8.1
python-jwt==3.3.0
python-Levenshtein==0.12.0
pytz==2020.4
PyYAML==5.3.1
pyzmq==19.0.1
qtconsole==5.0.1
QtPy==1.9.0
requests @ file:///tmp/build/80754af9/requests_1592841827918/work
requests-oauthlib==1.3.0
requests-toolbelt==0.9.1
rpy2==3.3.6
rsa==4.0
s3transfer==0.3.3
scikit-learn==0.24.0
scipy==1.6.0
Send2Trash==1.5.0
six==1.15.0
SQLAlchemy==1.4.0b1
statsmodels==0.12.1
tables==3.6.1
tensorboard==2.2.1
tensorboard-plugin-wit==1.6.0
tensorflow==2.2.0
tensorflow-estimator==2.2.0
tensorqtl @ file:///data1/home/songxu/software/tensorqtl
termcolor==1.1.0
terminado==0.8.3
testpath==0.4.4
threadpoolctl==2.1.0
tinydb==4.3.0
toml==0.10.2
toolz==0.11.1
torch==1.7.0
tornado==6.0.4
tqdm==4.54.0
traitlets==4.3.3
typing-extensions==3.7.4.3
tzlocal==2.1
urllib3==1.25.9
wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work
webencodings==0.5.1
Werkzeug==1.0.1
widgetsnbextension==3.5.1
wrapt==1.12.1
xarray==0.16.1
zipp==3.1.0
zstandard==0.14.0

It's really long, thank you for checking.

[schae234]

Thanks, nothing too crazy looking in here. However, looks like there have been a lot of updates to sqlalchemy recently it could be worth trying an older version to see if its compatible with odo.

[XscapeCn]

OK, I will try it and report the result here later. Thank you.

[XscapeCn]

I have installed SQLAlchemy version==1.3.11and it can show the logo of Camoco. But it still have a error.

Error.  nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)usage: camoco [-h] [--version] [--debug] [--interactive] [--force] Available Commands ...

      ___           ___           ___           ___           ___           ___
     /  /\         /  /\         /__/\         /  /\         /  /\         /  /\
    /  /:/        /  /::\       |  |::\       /  /::\       /  /:/        /  /::\
   /  /:/        /  /:/\:\      |  |:|:\     /  /:/\:\     /  /:/        /  /:/\:\
  /  /:/  ___   /  /:/~/::\   __|__|:|\:\   /  /:/  \:\   /  /:/  ___   /  /:/  \:\
 /__/:/  /  /\ /__/:/ /:/\:\ /__/::::| \:\ /__/:/ \__\:\ /__/:/  /  /\ /__/:/ \__\:\
 \  \:\ /  /:/ \  \:\/:/__\/ \  \:\~~\__\/ \  \:\ /  /:/ \  \:\ /  /:/ \  \:\ /  /:/
  \  \:\  /:/   \  \::/       \  \:\        \  \:\  /:/   \  \:\  /:/   \  \:\  /:/
   \  \:\/:/     \  \:\        \  \:\        \  \:\/:/     \  \:\/:/     \  \:\/:/
    \  \::/       \  \:\        \  \:\        \  \::/       \  \::/       \  \::/
     \__\/         \__\/         \__\/         \__\/         \__\/         \__\/

Thank you for your help.

[schae234]

Hi @XscapeCn, can you see if setting your NUMEXPR_MAX_THREADS environmental variable to something higher? Before you run the camoco command try this command: export NUMEXPR_MAX_THREADS=64.

[XscapeCn]

Hi, this will still cause that error.But it doesn't matter, camoco run well. I'll look for other solutions. Thank you!