JoniColeman
commented
1 week ago This is a known issue with certain versions of python (see https://github.com/conda/conda/issues/6018). It can be resolved by running:
export PYTHONNOUSERSITE=Trueand then running the command.
Hi Ollie,
Following the installation instructions, installation fails at the dependencies stage as follows:
(genopred) k1204688@erc-hpc-comp186:~/sgdp_coleman/Software/GenoPred/pipeline$ snakemake -j 1 --use-conda --conda-frontend mamba install_r_packages Building DAG of jobs... Traceback (most recent call last): File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exception_handler.py", line 17, in call return func(*args, **kwargs) File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/cli/main.py", line 51, in main_subshell from .conda_argparse import do_call, generate_parser, generate_pre_parser File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 50, in
from .main_create import configure_parser as configure_parser_create
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/cli/main_create.py", line 11, in
from ..notices import notices
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/notices/init.py", line 3, in
from .core import notices # noqa: F401
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/notices/core.py", line 14, in
from . import cache, fetch, views
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/notices/cache.py", line 25, in
from ..utils import ensure_dir_exists
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/utils.py", line 23, in
from .gateways.disk.read import compute_sum
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/gateways/disk/read.py", line 31, in
from ...exceptions import CondaUpgradeError, CondaVerificationError, PathNotFoundError
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exceptions.py", line 16, in
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/users/k1204688/.local/lib/python3.8/site-packages/requests/exceptions.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/users/k1204688/.conda/envs/genopred/bin/conda", line 13, in
sys.exit(main())
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/cli/main.py", line 128, in main
return conda_exception_handler(main, *args, *kwargs)
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exception_handler.py", line 388, in conda_exception_handler
return_value = exception_handler(func, args, kwargs)
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exception_handler.py", line 20, in call
return self.handle_exception(exc_val, exc_tb)
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exception_handler.py", line 51, in handle_exception
from .exceptions import (
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/site-packages/conda/exceptions.py", line 16, in
from requests.exceptions import JSONDecodeError
ImportError: cannot import name 'JSONDecodeError' from 'requests.exceptions' (/users/k1204688/.local/lib/python3.8/site-packages/requests/exceptions.py)
Traceback (most recent call last):
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/init.py", line 726, in snakemake
success = workflow.execute(
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/workflow.py", line 978, in execute
dag.create_conda_envs(
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/dag.py", line 313, in create_conda_envs
env.create(dryrun)
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 391, in create
pin_file = self.pin_file
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/common/init.py", line 192, in get
value = self.method(instance)
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 107, in pin_file
f".{self.conda.platform}.pin.txt"
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/common/init.py", line 192, in get
value = self.method(instance)
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 102, in conda
return Conda(self._container_img)
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 648, in init
shell.check_output(
File "/users/k1204688/.local/lib/python3.8/site-packages/snakemake/shell.py", line 63, in check_output
return sp.check_output(cmd, shell=True, executable=executable, kwargs)
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/subprocess.py", line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/users/k1204688/.conda/envs/genopred/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'conda info --json' returned non-zero exit status 1.
Not really clear to me why this happens – I'll find a work-around on CREATE and report back, but wanted to flag this as a bug to be solved. I think other answers here may solve this - I will check that.