I've just reinstalled rpy2 with Python3.5 and I am having difficulty figuring out why the module cannot find the "R-Home". I have installed R on my computer already. Should I try reinstalling R or another method? Some help would be much appreciated here!
import rpy2.rinterface
Traceback (most recent call last):
File "<ipython-input-7-676c977874d9>", line 1, in <module>
import rpy2.rinterface
File "/Users/JasonDucker/anaconda/lib/python3.5/site-packages/rpy2/rinterface/__init__.py", line 16, in <module>
tmp = subprocess.check_output(("R", "RHOME"), universal_newlines=True)
File "/Users/JasonDucker/anaconda/lib/python3.5/subprocess.py", line 629, in check_output
**kwargs).stdout
File "/Users/JasonDucker/anaconda/lib/python3.5/subprocess.py", line 696, in run
with Popen(*popenargs, **kwargs) as process:
File "/Users/JasonDucker/anaconda/lib/python3.5/subprocess.py", line 950, in __init__
restore_signals, start_new_session)
File "/Users/JasonDucker/anaconda/lib/python3.5/subprocess.py", line 1544, in _execute_child
raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: 'R'
This means that there is no executable in the PATH when python is calling "R RHOME" in a subprocess.
To overcome this add the path to R to your PATH. For example:
export PATH=/usr/local/some/place/bin:${PATH}
Related
I have a python script which is basically a graphic interface (pysimpleguy) to a mysql database.
I am working in python 3.8; my dependencies are:
PySimpleGUI 4.55.1
sqlalchemy 1.3.20
pymysql 1.0.2
pandas 1.1.3
regex 2020.10.15
pillow 8.0.1
The code works and I'd like to compile it to .exe to distribute it to users in my organization.
I tried to compile it with:
pyinstaller -D .\db_interface_v3.6.1_release.py --debug=imports
However, pyinstaller throws some errors when compiling:
201667 INFO: Building COLLECT COLLECT-00.toc
Traceback (most recent call last):
File "c:\users\spit\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "c:\users\spit\anaconda3\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "C:\Users\Spit\anaconda3\Scripts\pyinstaller.exe\__main__.py", line 7, in <module>
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\__main__.py", line 124, in run
run_build(pyi_config, spec_file, **vars(args))
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\__main__.py", line 58, in run_build
PyInstaller.building.build_main.main(pyi_config, spec_file, **kwargs)
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\building\build_main.py", line 782, in main
build(specfile, kw.get('distpath'), kw.get('workpath'), kw.get('clean_build'))
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\building\build_main.py", line 714, in build
exec(code, spec_namespace)
File "C:\Users\Spit\Desktop\DIPEx db parser\db_interface_v3.6.1_release.spec", line 37, in <module>
coll = COLLECT(exe,
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\building\api.py", line 818, in __init__
self.__postinit__()
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\building\datastruct.py", line 155, in __postinit__
self.assemble()
File "c:\users\spit\anaconda3\lib\site-packages\PyInstaller\building\api.py", line 866, in assemble
shutil.copy(fnm, tofnm)
File "c:\users\spit\anaconda3\lib\shutil.py", line 415, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "c:\users\spit\anaconda3\lib\shutil.py", line 261, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Spit\\Desktop\\DIPEx db parser\\dist\\db_interface_v3.6.1_release\\share\\jupyter\\lab\\staging\\node_modules\\.cache\\terser-webpack-p
lugin\\content-v2\\sha512\\2e\\ba\\cfce62ec1f408830c0335f2b46219d58ee5b068473e7328690e542d2f92f2058865c600d845a2e404e282645529eb0322aa4429a84e189eb6b58c1b97c1a'
If I try to run the compiled exe, I get an error regarding a specific .dll:
INTEL MKL ERROR: Impossibile trovare il modulo specificato. mkl_intel_thread.dll.
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll.
If I take this missing .dll from my Anaconda environment and copy it into the program's folder, when I try to run the .exe again it just dies without further messages:
import 'numpy.ma' # <pyimod03_importers.FrozenImporter object at 0x000001F6A455BEE0>
PS C:\Users\Spit\Desktop\DIPEx db parser\dist\db_interface_v3.6.1_release>
Any idea on how to sort it out?
Thanks!
Sorted out. As a future reference if someone stumbles upon this question, the error is caused by Windows' PATH_MAX limitation, preventing pyinstaller to find all the necessary files.
In order to disable said limitation: https://learn.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=cmd
Kudos to https://github.com/bwoodsend
I am trying to build an executable with pyinstaller and I am getting the following errors:
Traceback (most recent call last):
File "transformers/utils/versions.py", line 105, in require_version
File "importlib/metadata.py", line 551, in version
File "importlib/metadata.py", line 524, in distribution
File "importlib/metadata.py", line 187, in from_name
importlib.metadata.PackageNotFoundError: regex
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "chatbot2.py", line 8, in <module>
File "PyInstaller/loader/pyimod03_importers.py", line 546, in exec_module
File "transformers/__init__.py", line 43, in <module>
File "PyInstaller/loader/pyimod03_importers.py", line 546, in exec_module
File "transformers/dependency_versions_check.py", line 41, in <module>
File "transformers/utils/versions.py", line 120, in require_version_core
File "transformers/utils/versions.py", line 107, in require_version
importlib.metadata.PackageNotFoundError: The 'regex!=2019.12.17' distribution was not found and is required by this application.
Try: pip install transformers -U or pip install -e '.[dev]' if you're working with git master
[30391] Failed to execute script 'chatbot2' due to unhandled exception!
I am using PyInstaller version 5.0.dev0 and Python version 3.9.1.
I tried pip3.9 install transformers, pip3.9 install regex, I tried adding hooks hook-regex.py and hook-transformers.py.
I would really appreciate any suggestions! Thank you!
This question already has answers here:
Issues with pyinstaller and pyproj
(3 answers)
Closed 2 years ago.
My code works well when it's .py
but when I make .exe file with pyinstaller, it shows ModuleNotFoundError.
I write this when I made .exe
pyinstaller -F MyCode.py
How can I solve this problem?
I've read
Issues with pyinstaller and pyproj
and I was going to try to make and located hook-pyproj.py at "hooks" folder in Pyinstaller. but hook-pyproj.py was already there with the same code.
After that, I installed "basemap" and tried to use pyproj from it. However it shows me the same error.
This is the error it showed me when I execute the .exe file.
(I covered some information with *****)
Traceback (most recent call last):
File "collect\MyCode.py", line 8, in <module>
File "c:\users\*****\appdata\local\programs\python\python36-32\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 627, in exec_module
exec(bytecode, module.__dict__)
File "site-packages\mpl_toolkits\basemap\__init__.py", line 41, in <module>
File "c:\users\*****\appdata\local\programs\python\python36-32\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 627, in exec_module
exec(bytecode, module.__dict__)
File "site-packages\pyproj\__init__.py", line 62, in <module>
File "c:\users\*****\appdata\local\programs\python\python36-32\lib\site-packages\PyInstaller\loader\pyimod03_importers.py", line 627, in exec_module
exec(bytecode, module.__dict__)
File "site-packages\pyproj\crs.py", line 26, in <module>
File "pyproj\_crs.pyx", line 1, in init pyproj._crs
ModuleNotFoundError: No module named 'pyproj._datadir'
[25936] Failed to execute script MyCode
This is my code.
from mpl_toolkits.basemap import pyproj as pyproj
I tried this at first.
import pyproj
but I get same " ModuleNotFoundError: No module named 'pyproj._datadir' " error.
It's a bit odd and I don't exactly understand why but I found a quick dirty fix.
You can add this import
from pyproj import _datadir, datadir
to your existing one.
I noticed this pyproj import dll error error occurred on some Windows machines and not others.
Turned out to be a dependency on Visual C Runtime 2015+
https://support.microsoft.com/en-au/help/2977003/the-latest-supported-visual-c-downloads
I am trying to configure remote logging with Azure blob.
Airflow version: 1.10.2
Python: 3.6.5
Ubuntu: 18.04
Following are the step I did:
In $AIRFLOW_HOME/config/log_config.py, I have put REMOTE_BASE_LOG_FOLDER = 'wasb-airflow-logs' (This is a folder inside the container (container name: airflow-logs))
Empty init.py is in $AIRFLOW_HOME/config/
$AIRFLOW_HOME/config/ is added in $PYTHONPATH
Renamed DEFAULT_LOGGING_CONFIG to LOGGING CONFIG everywhere in $AIRFLOW_HOME/config/log_config.py
User defined in Airflow blob connection has read/write access to REMOTE_BASE_LOG_FOLDER
$AIRFLOW_HOME/airflow.cfg it has remote_logging = True
logging_config_class = log_config.LOGGING_CONFIG
remote_log_conn_id =
Following is the error:
Unable to load the config, contains a configuration error.
Traceback (most recent call last):
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 382, in resolve
found = getattr(found, frag)
AttributeError: module 'airflow.utils.log' has no attribute 'wasb_task_handler'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 384, in resolve
self.importer(used)
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/utils/log/wasb_task_handler.py", line 23, in <module>
from airflow.contrib.hooks.wasb_hook import WasbHook
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/contrib/hooks/wasb_hook.py", line 22, in <module>
from airflow.hooks.base_hook import BaseHook
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/hooks/base_hook.py", line 28, in <module>
from airflow.models import Connection
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/models.py", line 86, in <module>
from airflow.utils.dag_processing import list_py_file_paths
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/utils/dag_processing.py", line 49, in <module>
from airflow.settings import logging_class_path
ImportError: cannot import name 'logging_class_path'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 558, in configure
handler = self.configure_handler(handlers[name])
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 708, in configure_handler
klass = self.resolve(cname)
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 391, in resolve
raise v
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 384, in resolve
self.importer(used)
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/utils/log/wasb_task_handler.py", line 23, in <module>
from airflow.contrib.hooks.wasb_hook import WasbHook
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/contrib/hooks/wasb_hook.py", line 22, in <module>
from airflow.hooks.base_hook import BaseHook
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/hooks/base_hook.py", line 28, in <module>
from airflow.models import Connection
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/models.py", line 86, in <module>
from airflow.utils.dag_processing import list_py_file_paths
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/utils/dag_processing.py", line 49, in <module>
from airflow.settings import logging_class_path
ValueError: Cannot resolve 'airflow.utils.log.wasb_task_handler.WasbTaskHandler': cannot import name 'logging_class_path'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gsingh/venv/bin/airflow", line 21, in <module>
from airflow import configuration
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/__init__.py", line 36, in <module>
from airflow import settings, configuration as conf
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/settings.py", line 262, in <module>
logging_class_path = configure_logging()
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/logging_config.py", line 73, in configure_logging
raise e
File "/home/gsingh/venv/lib/python3.6/site-packages/airflow/logging_config.py", line 68, in configure_logging
dictConfig(logging_config)
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 795, in dictConfig
dictConfigClass(config).configure()
File "/home/gsingh/anaconda3/lib/python3.6/logging/config.py", line 566, in configure
'%r: %s' % (name, e))
ValueError: Unable to configure handler 'processor': Cannot resolve 'airflow.utils.log.wasb_task_handler.WasbTaskHandler': cannot import name 'logging_class_path'
I am not sure which configuration I am missing. Has anyone faced the same issue?
You need to install the azure package.
pip install 'apache-airflow[azure_blob_storage,azure_data_lake,azure_cosmos,azure_container_instances]
As per updating.md
This now should be installed with
pip install apache-airflow[azure]
But this didn't work for me.
sudo chown 50000:0 dags logs plugins in my case.
I tried to run official docker-compose.yml with all these containers (which are dependent on these 3 volume forwards) or simply wrap airflow standalone into a single container for a debug purpose. Turned out volumes were created with root ownerships instead of airflows.
I had the same error however if I scrolled up higher I could see that there was another exception thrown before the ValueError. Which was a PermissionError.
PermissionError: [Errno 13] Permission denied: '/usr/local/airflow/logs/scheduler'
The reason I got that error is because I didn't create the initial 3 folders (dags, logs, plugins) before running airflow docker container. So docker seems to have created then automatically but the permissions were wrong.
Steps to fix:
Stop current container
docker-compose down --volumes --remove-orphans
Delete folders dags, logs, plugins
Just in case Destroy the images and volumes already created (in Docker Desktop)
Create folders again from command line
mkdir logs dags plugins
run airflow docker again
docker-compose up airflow-init
docker-compose up
I've just installed a new plone 4.3 instance in a folder which already contained 2 Plone 4.3 instance, which both work fine. When I try to run buildout I get this error:
Traceback (most recent call last):
File "bin/buildout", line 17, in <module>
import zc.buildout.buildout
File "/usr/local/Plone4.3/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/buildout.py", line 40, in <module>
import zc.buildout.download
File "/usr/local/Plone4.3/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/download.py", line 20, in <module>
from zc.buildout.easy_install import realpath
File "/usr/local/Plone4.3/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/easy_install.py", line 31, in <module>
import setuptools.package_index
File "/usr/local/Plone4.3/Python-2.7/lib/python2.7/site-packages/distribute-0.6.35-py2.7.egg/setuptools/package_index.py", line 158, in <module>
sys.version[:3], require('distribute')[0].version
File "/usr/local/Plone4.3/buildout-cache/eggs/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 666, in require
continue # try the next older version of project
File "/usr/local/Plone4.3/buildout-cache/eggs/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 565, in resolve
pkg_resources.DistributionNotFound: distribute
Google has failed me. Can anyone tell me how to resolve this error?