I've installed all per-requisites from. Build fails with the following error by using ./waf command.
Traceback (most recent call last):
File "/usr/lib/python3.6/py_compile.py", line 125, in compile
_optimize=optimize)
File "<frozen importlib._bootstrap_external>", line 741, in source_to_code
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/lib/python3/dist-packages/visualizer/visualizer/svgitem.py", line 123
raise AttributeError, 'unknown property %s' % pspec.name
^
SyntaxError: invalid syntax
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/usr/lib/python3.6/py_compile.py", line 129, in compile
raise py_exc
py_compile.PyCompileError: File "/usr/local/lib/python3/dist-packages/visualizer/visualizer/svgitem.py", line 123
raise AttributeError, 'unknown property %s' % pspec.name
^
SyntaxError: invalid syntax
I will appreciate any help. Thank you.
You can disable python. First you need to clean your previous failed build and then configure by disabling the python.
./waf distclean
./waf --disable-python configure
./waf
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 using Apache Zeppelin. My anaconda version is conda 4.8.4. and my spark version is:
%spark2.pyspark
spark.version
u'2.3.1.3.0.1.0-187'
When I run my code, it throws followed error:
Exception AttributeError: "'StringIndexer' object has no attribute '_java_obj'" in <object repr() failed> ignored
Fail to execute line 4: indexerFeatures = StringIndexer(inputCols=catColumns, outputCols=catIndexedColumns, handleInvalid="keep")
Traceback (most recent call last):
File "/tmp/zeppelin_pyspark-66369397479549554.py", line 375, in <module>
exec(code, _zcUserQueryNameSpace)
File "<stdin>", line 4, in <module>
File "/usr/hdp/current/spark2-client/python/lib/pyspark.zip/pyspark/__init__.py", line 105, in wrapper
return func(self, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'outputCols'
I ran the same code in Databricks and everything worked fine. I also checked the import for the StringIndexer with the help() function and it didn't included the outputCols argument.
It should be outputCol, not outputCols.
For spark 2.3.1, you can refer to: https://spark.apache.org/docs/2.3.1/api/python/pyspark.ml.html#pyspark.ml.feature.StringIndexer
class pyspark.ml.feature.StringIndexer(inputCol=None, outputCol=None, handleInvalid='error', stringOrderType='frequencyDesc')
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 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?
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?