I'm trying to use PuDB with ipython as the shell, but when I drop to shell, I get the following error:
can't set attribute
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Error in sys.exitfunc:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Version details:
PuDB 2011.3.1
IPython 0.12
Python 2.7.1
Mac OS X 10.7.3
This is a known issue, and should be fixed in IPython 0.12.1 or master. Does updating to current (0.12.1) IPython help?
Related
I deleted the anaconda directory under the home and bashrc configurations.
Now, I need to install it again, but it occurs a problem evenif overwrites unsuccessful installation on Linux.
Should I delete some additional config files? How can I handle this?
sh Downloads/Anaconda3-2022.10-Linux-x86_64.sh -u -p /home/user/anaconda3/
PREFIX=/home/user/anaconda3
Unpacking payload ...
concurrent.futures.process._RemoteTraceback:
'''
Traceback (most recent call last):
File "concurrent/futures/process.py", line 384, in wait_result_broken_or_wakeup
File "multiprocessing/connection.py", line 256, in recv
TypeError: __init__() missing 1 required positional argument: 'msg'
'''
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "entry_point.py", line 69, in <module>
File "concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
File "concurrent/futures/_base.py", line 608, in result_iterator
File "concurrent/futures/_base.py", line 445, in the result
File "concurrent/futures/_base.py", line 390, in __get_result
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
[8382] Failed to execute script entry_point
Make sure deleted .conda directory under home and have enough disk space.
No need to delete .cache or any bin libraries.
I am just getting started on Python, though I know a bit of R. I want to replicate something someone has already done. I am receiving this error on one of my kernels on Jupyter and I don't immediately know what to do about it. Does anyone have any input or experience with it?
Traceback (most recent call last):
File "parse.py", line 8, in <module>
from param import ranked_blast_output_schema, blast_outfmt6_schema
ImportError: cannot import name 'ranked_blast_output_schema' from 'param' (/Users/myaccount/miniconda3/lib/python3.8/site-packages/param/__init__.py)
Traceback (most recent call last):
File "lca_analysis.py", line 52, in <module>
if ("~" in blast_results["query"].iloc[0]):
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 894, in __getitem__
return self._getitem_axis(maybe_callable, axis=axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1500, in _getitem_axis
self._validate_integer(key, axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1443, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
Ah okay. I am replicating a Jupyter notebook and I was told to run this link on bash.
lca_analysis.py --blast_type nt --fpath s3://org_name/contigs/CMS001_002_Ra_S1/blast_nt.m9 --filtered_blast_path s3://bucket_name/contig_quality/CMS001_002_Ra_S1/blast_nt_filtered.m9 --excluded_contigs_path s3://bucket_name/contig_quality/CMS001_002_Ra_S1/exclude_contigs_nt.txt --outpath s3://bucket_name/contig_quality/CMS001_002_Ra_S1/lca_nt.m9 --read_count_path s3://bucket_name/contigs/CMS001_002_Ra_S1/contig_stats.json --verbose True
But then, I had this error
Read counts have been loaded: s3://bucket_name/contigs/CMS001_002_Ra_S1/contig_stats.json| elapsed time: 0.73 seconds
/var/folders/ns/gdtc2hvx1g13_29wct4qkhd80000gq/T/tmp3m3k6w9o blast file downloaded to this tempfile
Traceback (most recent call last):
File "parse.py", line 8, in <module>
from param import ranked_blast_output_schema, blast_outfmt6_schema
ImportError: cannot import name 'ranked_blast_output_schema' from 'param' (/Users/myaccount/miniconda3/lib/python3.8/site-packages/param/__init__.py)
Traceback (most recent call last):
File "lca_analysis.py", line 52, in <module>
if ("~" in blast_results["query"].iloc[0]):
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 894, in __getitem__
return self._getitem_axis(maybe_callable, axis=axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1500, in _getitem_axis
self._validate_integer(key, axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1443, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
I had just used pip install param to get param, and the install went just fine.
I am trying to follow instruction from Enthought support website To test of what I have done i run line:
_python.exe canopy-script.pyw -d
Unfortunately this gives Traceback:
Traceback (most recent call last):
File "canopy-script.pyw", line 776, in <module>
File "canopy-script.pyw", line 336, in bootstrap
File "canopy-script.pyw", line 363, in chainload
File "canopy-script.pyw", line 762, in _chainload
File "C:\Users\User\AppData\Local\Enthought\Canopy\App\appdata\canopy-1.7.4.3348.win-x86_64\Canopy-script.pyw", line 7, in <module>
from canopy.app.bootstrap import main
ImportError: No module named canopy.app.bootstrap
After "Search" I can see many of bootstrap.py files on the disc.
What would be the solution for this problem?
The current version of Canopy is 2.1.9. (You are running v 1.7.4).
To update Canopy, and for a link to release notes, please see "Installing a new Canopy version".
After you update, see:
https://support.enthought.com/hc/en-us/articles/360021798791--UnresolvableRequirements-or-Conflicting-requirements-when-installing-or-updating-packages
I'm setting up awslogs agent on ec2 instance, When i run the python script of awslogs. I'm getting below message.
Downloading the latest CloudWatch Logs agent bits ... ERROR: Failed to create virtualenv. Try manually installing with pip and adding it to the sudo user's PATH before running this script.
And awslogs-agent-setup.log show below error.
Environment: CentOS 6.10 and Python 2.6
Traceback (most recent call last):
File "/usr/bin/pip", line 7, in <module>
from pip._internal import main
File "/usr/lib/python2.6/site-packages/pip-19.0.3-py2.6.egg/pip/_internal/__init__.py", line 19, in <module>
from pip._vendor.urllib3.exceptions import DependencyWarning
File "/usr/lib/python2.6/site-packages/pip-19.0.3-py2.6.egg/pip/_vendor/urllib3/__init__.py", line 8, in <module>
from .connectionpool import (
File "/usr/lib/python2.6/site-packages/pip-19.0.3-py2.6.egg/pip/_vendor/urllib3/connectionpool.py", line 92
_blocking_errnos = {errno.EAGAIN, errno.EWOULDBLOCK}
^
SyntaxError: invalid syntax
/usr/bin/virtualenv
Traceback (most recent call last):
File "/usr/bin/virtualenv", line 7, in <module>
from virtualenv import main
File "/usr/lib/python2.6/site-packages/virtualenv.py", line 51, in <module>
print("ERROR: {}".format(sys.exc_info()[1]))
ValueError: zero length field name in format
Basically, this error is due to your python version 2.6. Could you please update your python version from 2.6 to 2.7 or 3.1.
This should help.
I just installed gsutil on OS X, exactly following Google's instruction, and am seeing errors of the following format when running any gsutil command:
Traceback (most recent call last):
File "/Users//gsutil/gsutil", line 22, in <module>
gsutil.RunMain()
File "/Users//gsutil/gsutil.py", line 101, in RunMain
sys.exit(gslib.__main__.main())
File "/Users//gsutil/gslib/__main__.py", line 175, in main
command_runner = CommandRunner()
File "/Users//gsutil/gslib/command_runner.py", line 107, in __init__
self.command_map = self._LoadCommandMap()
File "/Users//gsutil/gslib/command_runner.py", line 113, in _LoadCommandMap
__import__('gslib.commands.%s' % module_name)
File "/Users//gsutil/gslib/commands/disablelogging.py", line 16, in <module>
from gslib.command import COMMAND_NAME
ImportError: cannot import name COMMAND_NAME
This error occurs on several modules in the commands directory. The only thing I could do to get rid of these errors is to remove the following modules from the directory which reference COMMAND_NAME: disablelogging, enablelogging, getacl, getcors, getdefacl, getlogging, setacl, setcors, setdefacl.
Did I do the right thing here? Is this a bug in gsutil?