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The command starts to run and the "Loading recipes" progress bar starts to fill. When it's done, it raises the following error:
13:38:14 BIOCONDA INFO Building Recipe DAG: done (6761 nodes, 20306 edges)
13:38:14 BIOCONDA ERROR Dropping into debugger
Traceback (most recent call last):
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 71, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-17>", line 5, in autobump
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 90, in wrapper
func(*args, **kwargs)
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 847, in autobump
config_dict, cache_fn=cache and cache + "_dag.pkl")
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/autobump.py", line 133, in __init__
self.dag = graph.filter_recipe_dag(self.dag, packages, exclude)
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/graph.py", line 127, in filter_recipe_dag
and not any(fnmatch(recipe.reldir, p) for p in exclude)):
TypeError: 'NoneType' object is not iterable
Traceback (most recent call last):
File "/Users/vini/anaconda3/envs/bioconda-utils/bin/bioconda-utils", line 10, in <module>
sys.exit(main())
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 971, in main
bioconductor_skeleton, clean_cran_skeleton, autobump, bot
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/argh/dispatching.py", line 328, in dispatch_commands
dispatch(parser, *args, **kwargs)
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/argh/dispatching.py", line 260, in _call
result = function(*positional, **keywords)
File "<boltons.funcutils.FunctionBuilder-20>", line 5, in autobump
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 130, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-19>", line 5, in autobump
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 59, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-18>", line 5, in autobump
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 71, in wrapper
func(*args, **kwargs)
File "<boltons.funcutils.FunctionBuilder-17>", line 5, in autobump
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 90, in wrapper
func(*args, **kwargs)
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/cli.py", line 847, in autobump
config_dict, cache_fn=cache and cache + "_dag.pkl")
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/autobump.py", line 133, in __init__
self.dag = graph.filter_recipe_dag(self.dag, packages, exclude)
File "/Users/vini/anaconda3/envs/bioconda-utils/lib/python3.7/site-packages/bioconda_utils/graph.py", line 127, in filter_recipe_dag
and not any(fnmatch(recipe.reldir, p) for p in exclude)):
TypeError: 'NoneType' object is not iterable
I tried reinstalling bioconda-utils a few times, but to no avail. Any ideas on how to proceed?
Thank you for any assistance you can provide,
V
The text was updated successfully, but these errors were encountered:
vinisalazar
changed the title
Error when trying to run bioconda-utils
TypeError when trying to run bioconda-utils
Jan 11, 2021
Definitely seems like a bug. This is mostly run as a cron job without specifying --packages (the source of the bot's PRs), so I imagine there's some issue with how --packages bioprov is being handled.
Hi, I installed
bioconda-utils
as instructed on this page.When I run the following command:
bioconda-utils autobump recipes/ config.yml --packages bioprov
The command starts to run and the "Loading recipes" progress bar starts to fill. When it's done, it raises the following error:
I tried reinstalling bioconda-utils a few times, but to no avail. Any ideas on how to proceed?
Thank you for any assistance you can provide,
V
The text was updated successfully, but these errors were encountered: