Interestingly, on my machine (OSX) importing the package hgvs runs smoothly, even though I'm working on python 2.7 (and ExtendedInterpolation is a python 3 function from configparser). As far as what I've gathered, it simply uses a backport of Python 3's configparser module, so it should work anyways if Python 3 is installed.
However, the following error occurs when I try to import the module on a EC2 instace using iPython Notebook.
Any ideas of what may be causing the issue?
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-60-832dbede7fbb> in <module>()
----> 1 import hgvs.location
/usr/local/lib/python2.7/dist-packages/hgvs/hgvs/__init__.py in <module>()
57 import warnings
58
---> 59 from .config import global_config # flake8: noqa; importing symbol
60
61 logger = logging.getLogger(__name__)
/usr/local/lib/python2.7/dist-packages/hgvs/hgvs/config.py in <module>()
22 from __future__ import absolute_import, division, print_function, unicode_literals
23
---> 24 from configparser import ConfigParser, ExtendedInterpolation
25 from copy import copy
26 import logging
ImportError: cannot import name ExtendedInterpolation
According to this the problem is that:
Unfortunately in 0.14.0 they broke the configparser import by introducing their own.
To resolve it, I downgraded the future library:
pip install future==0.13.1
Related
I am using jupyter Notebook(conda root). The python version I am running is 2.7
I am having a hard time getting wordcloud installed into my environment. Here's the code
from wordcloud import WordCloud
But I got this error:
ImportErrorTraceback (most recent call last)
<ipython-input-21-8038e19af624> in <module>()
----> 1 from wordcloud import WordCloud
C:\Users\aneeq\Anaconda2\lib\site-packages\wordcloud\__init__.py in <module>()
----> 1 from .wordcloud import (WordCloud, STOPWORDS, random_color_func,
2 get_single_color_func)
3 from .color_from_image import ImageColorGenerator
4
5 __all__ = ['WordCloud', 'STOPWORDS', 'random_color_func',
C:\Users\aneeq\Anaconda2\lib\site-packages\wordcloud\wordcloud.py in <module>()
17 from operator import itemgetter
18
---> 19 from PIL import Image
20 from PIL import ImageColor
21 from PIL import ImageDraw
C:\Users\aneeq\Anaconda2\lib\site-packages\PIL\Image.py in <module>()
56 # Also note that Image.core is not a publicly documented interface,
57 # and should be considered private and subject to change.
---> 58 from . import _imaging as core
59 if PILLOW_VERSION != getattr(core, 'PILLOW_VERSION', None):
60 raise ImportError("The _imaging extension was built for another "
**ImportError: DLL load failed: The specified module could not be found.**
Can anyone explain what is this error?
I need to use world cloud for my homework assignment
You have problem with part of python Pillow module: with a library, that builds from _imaging.c. Try to reinstall python Pillow module from .exe package, not with pip.
I am trying to import beakerx into my jupyter environment like so:
from beakerx import *
However, I get the following error:
ImportError Traceback (most recent call last)
<ipython-input-19-4c368a35c7cf> in <module>()
----> 1 from beakerx import *
/Users/vivaksoni1/venv/lib/python2.7/site-packages/beakerx/__init__.py in <module>()
13 # limitations under the License.
14
---> 15 from .runtime import BeakerX
16 from .plot import *
17 from .easyform import *
/Users/vivaksoni1/venv/lib/python2.7/site-packages/beakerx/runtime.py in <module>()
16
17 import os, json, pandas, numpy
---> 18 import urllib.request, urllib.parse, urllib.error, urllib.request, urllib.error, urllib.parse, IPython, datetime, calendar, math, traceback, time
19 from traitlets import Unicode
20
ImportError: No module named request
I am not sure what this error means? Also, it seems to be looking into python2.7 directories even though this is a python 3 script? I installed beakerx using: pip3 install beakerx and can see the files in the right folder within the right folder:
anaconda3/pkgs/beakerx-0.12.2-py36_2/lib/python3.6/site-packages/beakerx
This seems to be how every other module is stored but I cannot get it working for some reason. Can anyone help?
I was using python's datashader 0.5.0 package to plot population density information, generally following the tutorial https://www.continuum.io/blog/developer-blog/analyzing-and-visualizing-big-data-interactively-your-laptop-datashading-2010-us . I installed datashader using conda install -c bokeh datashader=0.5.0.
All was fine. Though perhaps unrelated, things seemed to break as soon as I installed the haloviews and geoviews packages. After installing these additional packages, I can no longer import datashader and my once working code no longer runs. When importing datashader, I get the following error:
AttributeError: module 'snappy' has no attribute 'compress'
I am running on windows 10, anaconda python 3.5.3.
Perhaps I'm going down the wrong rabbit hole, but I thought perhaps it was the snappy package. I ran "conda install -c conda-forge snappy=1.1.4". conda list reveals that snappy is installed. Snappy does import. The snappy.compress object is not found. My issue seems related to the following SO post as I also had a fastparquet error when trying geoviews: error with snappy while importing fastparquet in python
When running import snappy, print(snappy.__filename__) gives the following error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-5-b8565733b383> in <module>()
----> 1 import snappy; print(snappy.__file__)
AttributeError: module 'snappy' has no attribute '__file__'
I also tried uninstalling through both conda and pip just in case. Still no joy.
Running "pip install python-snappy" results in a "failed building wheel for python-snappy" error preceded with " error: Microsoft Visual C++ 14.0 is required..." So I went and got the "Microsoft Visual C++ Redistributable for Visual Studio 2017" and ran it, but had no change.
Any thoughts on how to resolve this? For reference, the full error on datashader import is as follows:
--------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-7-3d7b1ff9e530> in <module>()
----> 1 import datashader
C:\Python\lib\site-packages\datashader\__init__.py in <module>()
3 __version__ = '0.5.0'
4
----> 5 from .core import Canvas
6 from .reductions import (count, any, sum, min, max, mean, std, var, count_cat,
7 summary)
C:\Python\lib\site-packages\datashader\core.py in <module>()
3 import numpy as np
4 from datashape.predicates import istabular
----> 5 from odo import discover
6 from xarray import DataArray
7
C:\Python\lib\site-packages\odo\__init__.py in <module>()
63 from .backends.url import URL
64 with ignoring(ImportError):
---> 65 from .backends.dask import dask
66
67
C:\Python\lib\site-packages\odo\backends\dask.py in <module>()
8
9 from dask.array.core import Array, from_array
---> 10 from dask.bag.core import Bag
11 import dask.bag as db
12 from dask.compatibility import long
C:\Python\lib\site-packages\dask\bag\__init__.py in <module>()
1 from __future__ import absolute_import, division, print_function
2
----> 3 from .core import (Bag, Item, from_sequence, from_url, to_textfiles, concat,
4 from_delayed, map_partitions, bag_range as range,
5 bag_zip as zip, bag_map as map)
C:\Python\lib\site-packages\dask\bag\core.py in <module>()
30
31 from ..base import Base, normalize_token, tokenize
---> 32 from ..bytes.core import write_bytes
33 from ..compatibility import apply, urlopen
34 from ..context import _globals, defer_to_globals
C:\Python\lib\site-packages\dask\bytes\__init__.py in <module>()
2
3 from ..utils import ignoring
----> 4 from .core import read_bytes, open_files, open_text_files
5
6 from . import local
C:\Python\lib\site-packages\dask\bytes\core.py in <module>()
7 from warnings import warn
8
----> 9 from .compression import seekable_files, files as compress_files
10 from .utils import (SeekableFile, read_block, infer_compression,
11 infer_storage_options, build_name_function)
C:\Python\lib\site-packages\dask\bytes\compression.py in <module>()
30 with ignoring(ImportError):
31 import snappy
---> 32 compress['snappy'] = snappy.compress
33 decompress['snappy'] = snappy.decompress
34
AttributeError: module 'snappy' has no attribute 'compress'
It turns out that in adding packages, something messed up the snappy install. I followed this solution: How to install snappy C libraries on Windows 10 for use with python-snappy in Anaconda?
It was a snappy error, not a datashader issue, but I'll leave the post in case anyone has the same series of issues.
I am having trouble importing tika in a python file. I have spent a lot of time googling and been unable to find anything. Here is the iPython command: import tika, and subsequent stack trace.
It occurs to me that there could be a problem with a module on which tika is dependent, such as requests, or urllib3. However, when I try to install those with pip, it says requirement already satisfied. I have also double checked the PYTHONHOME director, and I'm 99% sure it's correct.
$ ipython
Python 3.6.1 (v3.6.1:69c0db5, Mar 21 2017, 17:54:52) [MSC v.1900 32 bit (Intel)]
Type "copyright", "credits" or "license" for more information.
IPython 4.2.1 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
WARNING: Readline services not available or not loaded.
WARNING: Proper color support under MS Windows requires the pyreadline library.
You can find it at:
http://ipython.org/pyreadline.html
Defaulting color scheme to 'NoColor'
In [1]: import tika
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
C:\cygwin64\lib\python3.6\site-packages\requests\packages\__init__.py in <module>()
26 try:
---> 27 from . import urllib3
28 except ImportError:
ImportError: cannot import name 'urllib3'
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
<ipython-input-1-9f3de0ba3e70> in <module>()
----> 1 import tika
C:\cygwin64\lib\python3.6\site-packages\tika\tika.py in <module>()
18
19 try:
---> 20 __import__('pkg_resources').declare_namespace(__name__)
21 except ImportError:
22 from pkgutil import extend_path
C:\cygwin64\lib\python3.6\site-packages\pkg_resources\__init__.py in declare_namespace(packageName)
2161 # Ensure all the parent's path items are reflected in the child,
2162 # if they apply
-> 2163 _handle_ns(packageName, path_item)
2164
2165 finally:
C:\cygwin64\lib\python3.6\site-packages\pkg_resources\__init__.py in _handle_ns(packageName, path_item)
2096 path = module.__path__
2097 path.append(subpath)
-> 2098 loader.load_module(packageName)
2099 _rebuild_mod_path(path, packageName, module)
2100 return subpath
C:\cygwin64\lib\python3.6\site-packages\tika\tika.py in <module>()
89 open = codecs.open
90
---> 91 import requests
92 import socket
93 import tempfile
C:\cygwin64\lib\python3.6\site-packages\requests\__init__.py in <module>()
50 # Attempt to enable urllib3's SNI support, if possible
51 try:
---> 52 from .packages.urllib3.contrib import pyopenssl
53 pyopenssl.inject_into_urllib3()
54 except ImportError:
C:\cygwin64\lib\python3.6\site-packages\requests\packages\__init__.py in <module>()
27 from . import urllib3
28 except ImportError:
---> 29 import urllib3
30 sys.modules['%s.urllib3' % __name__] = urllib3
31
C:\cygwin64\lib\python3.6\site-packages\urllib3\__init__.py in <module>()
6 import warnings
7
----> 8 from .connectionpool import (
9 HTTPConnectionPool,
10 HTTPSConnectionPool,
C:\cygwin64\lib\python3.6\site-packages\urllib3\connectionpool.py in <module>()
9
10
---> 11 from .exceptions import (
12 ClosedPoolError,
13 ProtocolError,
C:\cygwin64\lib\python3.6\site-packages\urllib3\exceptions.py in <module>()
1 from __future__ import absolute_import
----> 2 from .packages.six.moves.http_client import (
3 IncompleteRead as httplib_IncompleteRead
4 )
5 # Base Exceptions
ValueError: source code string cannot contain null bytes
In case anyone else is looking at this, here is how I finally solved my issue.
I had been mistakenly assuming that the python-tika module was a fully packaged, ready to run version of tika. In fact, you need to download the java tika server from Apache, and it must be running when you use python-tika (you can easily just run the server on localhost).
The Python-tika module then allows you to make requests to this server from your python code. I probably should have known this but for some reason I didn't pick it up in the documentation.
Are you sure you have that module installed?
If not, just go to the Command Prompt and type pip install tika
I think here is a good approach for installing tika on the Windows:
First, install java SE from this link:
https://www.oracle.com/ca-en/java/technologies/javase-downloads.html
Second, install a specific version of tika:
pip install tika==1.23
Third, download and run the tika server and tika app files from apache:
https://archive.apache.org/dist/tika/tika-server-1.23.jar
https://archive.apache.org/dist/tika/tika-app-1.23.jar
it should be fine, and you should be able to run tika in your application.
I am trying to set up a Jupyter notebook server at home. It has taken me a long time, but I have build and installed Python 3.4 and all the required packages from FreeBSD ports successfully. The notebook server is up and running fine, except every time when I try to import numpy:
In[1]: import numpy
The following errors occur:
ImportError Traceback (most recent call last)
<ipython-input-1-5a0bd626bb1d> in <module>()
----> 1 import numpy
/usr/local/lib/python3.4/site-packages/numpy/__init__.py in <module>()
178 return loader(*packages, **options)
179
--> 180 from . import add_newdocs
181 __all__ = ['add_newdocs',
182 'ModuleDeprecationWarning',
/usr/local/lib/python3.4/site-packages/numpy/add_newdocs.py in <module>()
11 from __future__ import division, absolute_import, print_function
12
---> 13 from numpy.lib import add_newdoc
14
15 ###############################################################################
/usr/local/lib/python3.4/site-packages/numpy/lib/__init__.py in <module>()
6 from numpy.version import version as __version__
7
----> 8 from .type_check import *
9 from .index_tricks import *
10 from .function_base import *
/usr/local/lib/python3.4/site-packages/numpy/lib/type_check.py in <module>()
9 'common_type']
10
---> 11 import numpy.core.numeric as _nx
12 from numpy.core.numeric import asarray, asanyarray, array, isnan, \
13 obj2sctype, zeros
/usr/local/lib/python3.4/site-packages/numpy/core/__init__.py in <module>()
12 os.environ[envkey] = '1'
13 env_added.append(envkey)
---> 14 from . import multiarray
15 for envkey in env_added:
16 del os.environ[envkey]
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by /usr/local/lib/gcc48/libgfortran.so.3 not found
The error messages for importing pandas and matplotlib are different, but I suspect that has something to do with this numpy import error.
Strangely, all 3 packages work fine in Python and IPython consoles with no problems at all!
I have googled and made the following attempts:
delete and reinstall numpy -> no change
append numpy directory to sys.path -> no change
install a lot of other external packages just to see if it's only related to numpy -> they are all working fine in both consoles and notebook, except scipy giving some error related to numpy
Thank you for your help!
My gcc is version 4.2.1.
I have fixed this by setting the LD_LBRARY_PATH to /usr/local/lib/gcc48. gcc48 is already installed in my system.
To avoid setting the path every time, I've added the following line to /.cshrc:
setenv LD_LIBRARY_PATH /usr/local/lib/gcc48
edit:
This won't work is you want to start the notebook server automatically by adding to crontab:
#reboot /usr/local/bin/jupyter-notebook
the same error appears when trying to import numpy and modules depending on numpy
I fixed this by making a copy of /usr/local/bin/jupyter-notebook and added the following lines:
import sys
import re
----------------- add these 2 lines below --------------
import os
os.environ['LD_LIBRARY_PATH'] = '/usr/local/lib/gcc48'
....
Add the new file to crontab instead of jupyter-notebook.
The issue is not with your python modules. The error message at the bottom, where it says ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by /usr/local/lib/gcc48/libgfortran.so.3 not found indicates that it's a dependency error with the Fortran library. Apparently it wants gcc 4.6 or higher, and apparently you have a lower version installed. Not being familiar with Python libraries or your setup, my guess is that it could be an issue with /usr/ports/devel/py-fortran. I would recommend checking the gcc version on your machine with gcc -v and whatever fortran-related ports you have installed with pkg info and then take it from there.