I am doing bioinformatics that has biopython dependency. Biopython always give me the following error:
I hope someone could help me with this issue. Thank you!
I had a problem with this when biopython (as a dependency) was installed during the installation of another package. Solution:
pip uninstall biopython
pip install biopython
This can occur on Biopython version >= 1.72 and has been discussed on the biopython mailing list here. This error occurs when you try and import while inside the biopython/ directory, to fix the error simply move to another directory outside the source tree and then execute your code.
If the error still occurs then likely the install has not been setup properly, and you can try running the following standard installation steps (assuming you have not used pip) to get the files and directories in the correct places:
python setup.py build
python setup.py test # not compulsory for the fix
python setup.py install # add '--prefix' flag to install to a particular directory
We have improved the traceback for future biopython releases, see 8efbf6d:
ImportError: cannot import name '_aligners': you should not import directly from the biopython source directory; please exit the source tree and re-launch your code from there
Related
I'm running this command to install os_sys package:
pip3 install os_sys
but receiving this error:
ERROR: os-sys has an invalid wheel, could not read
'os_sys-1.9.3.dist-info/WHEEL' file: KeyError("There is no item named
'os_sys-1.9.3.dist-info/WHEEL' in the archive")
I already installed Wheel.
Thank you for any help.
Just ran into same issue. Actually, this package is already included in Python.
So, just use
import os
import sys
in your py script and this should work.
If this is still not working for you, try to make sure that you have installed only one version of Python, I ran into the same issue, and any os method I tried to use was not working for me at all.
What I have done: I deinstalled all the other versions, and then I made only one clean installation, also removed the Path entries related to the deinstalled older versions. Then it finally worked!
I'm running python code which uses the dlib module. I'm using arch linux, so I downloaded dlib from here: https://aur.archlinux.org/packages/dlib/
Then I try to import the dlib module, but it still doesn't work:
ModuleNotFoundError: No module named 'dlib'
Is there a dependency that I didn't download or am I downloading the wrong module? I can't figure out what the problem is, since I downloaded the official module already.
I fixed the problem, all you have to do is to search in your package manager if you are a linux user, and try importing dlib in your python code, if that didn't work, then download dlib from this link: https://sourceforge.net/projects/dclib/files/latest/download
extract the files, and run the setup.py files, it will take a while till it finishes, and that should make it work, you can now run codes using dlib library with no problems.
hope that helps someone :D.
I had a same issue, but you need to download it to your site-packpages of where your python is there for python-idle or if ur getting a download error in pycharm , I solved the error by downloading dlib from cmd to the venv of my pycharm.project directory command being install dlib--19.16.0 (current one) or you can download a .whl file which suits your python,processor configuration run dt .whl file and your good to go
I am trying to install the python submodule ANCA in my mac, for which I have run the following:
pip install git+https://github.com/acadev/anca.git
getting the following:
.
.
.
Installing collected packages: anca
Running setup.py install for anca ... done
Successfully installed anca-0.1.5
I have miniconda installed in my computer, and I have checked that the module and its files and dependencies are correctly located in /usr/local/miniconda2/lib/python2.7/site-packages/anca
When I import anca in my notebook it does not give me any error, but if I try to import a submodule it gives me the following error:
from anca import IterativeMeansAlign
ImportError: cannot import name IterativeMeansAlign
It is the same with other submodules, but all of them are apparently well installed with all their files.
I have also tried to install the package using Git:
git clone https://github.com/acadev/anca.git
sudo python setup.py install
with the same result.
Note: 'locate' is not able to locate the module anca unlike the rest of the python modules although I can see all the files in the right location. It is the first time this happens to me.
Thanks a lot for your help,
any suggestion will be very appreciated.
Edit: Yes I know this question already exists, except my question is a bit different and none of the solutions fixed it.
I do most of my Python stuff when I'm at work and not on my personal machine, but I decided to install it on my personal computer as well. I fresh installed python 3.6.1, and created a virtual environment with virtualenv. Then within the virtualenv I tried to pip install urllib (or any module) and I received the error:
(pdbot) C:\Users\user\Documents\pdbot>pip install urllib
Collecting urllib
Using cached urllib-1.21.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\user\AppData\Local\Temp\pip-build-50tn0wlb\urllib\setup.py", line 191
s.connect((base64.b64decode(rip), 017620))
^
SyntaxError: invalid token
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\user\AppData\Local\Temp\pip-build-50tn0wlb\urllib\
I read elsewhere that this error had something to do with setuptools not being properly installed. So I ran this to attempt to fix the issue:
easy_install -U setuptools
I ended up receiving an even weirder error next:
(pdbot) C:\Users\zeke\Documents\pdbot>easy_install -U setuptools
Searching for setuptools
Reading https://pypi.python.org/simple/setuptools/
Downloading https://pypi.python.org/packages/a9/23/720c7558ba6ad3e0f5ad01e0d6ea2288b486da32f053c73e259f7c392042/setuptools-36.0.1.zip#md5=430eb106788183eefe9f444a300007f0
Best match: setuptools 36.0.1
Processing setuptools-36.0.1.zip
Writing C:\Users\zeke\AppData\Local\Temp\easy_install-jhg1val_\setuptools-36.0.1\setup.cfg
Running setuptools-36.0.1\setup.py -q bdist_egg --dist-dir C:\Users\zeke\AppData\Local\Temp\easy_install-jhg1val_\setuptools-36.0.1\egg-dist-tmp-8apak7kn
warning: no files found matching '*' under directory 'setuptools\_vendor'
Copying setuptools-36.0.1-py3.6.egg to c:\users\zeke\documents\pdbot\lib\site-packages
Adding setuptools 36.0.1 to easy-install.pth file
Installing easy_install-script.py script to c:\users\zeke\documents\pdbot\Scripts
Installing easy_install.exe script to c:\users\zeke\documents\pdbot\Scripts
error: [WinError 5] Access is denied: 'c:\\users\\zeke\\documents\\pdbot\\Scripts\\easy_install.exe'
This looks like a permissions error, but I ran these both in an administrator command prompt (Windows 10) and got the same result. I am the only user on this computer and I have all admin permissions. Is this virtualenv causing an issue? How do I remedy it?
EDIT: I was able to fix the permissions issue by leveraging the python executable like so:
python -m easy_install -U setuptools
But it didn't fix the python setup.py egg_info issue. I still get this error message when trying to pip install anything:
Command "python setup.py egg_info" failed with error code 1 in C:\Users\user\AppData\Local\Temp\pip-build-50tn0wlb\urllib\
I have tried both python -m pip install urllib and pip install urllib and neither work.
I had the same problem when trying to install urllib, but after doing a pip search urllib, I discovered that the problem was due to the version of urllib. From the search:
$ pip search urllib
...
> urllib5 (5.0.0) - Just increment the number and create a new lib. Never fix the original one.
At the end, a simple
pip install urllib5
within an elevated shell solved it.
Your problem has to do with permissions. The related/similar tools setup_tools, easy_install, and pip all tend to set a default set of permissions on files and folders they try to create in the package installation folder(s), rather than trying to match access permissions of the location they're installing in.
On Linux systems, where files and folders individually have permissions, this is frequently bypassed with the sudo command. On Windows, the equivalent is to run the installer as an Administrator. Since you're in the console, you have to open a console with Administrator privileges to run the pip command in.
Notable under Windows, the modules installed with pip from an Administrator console are still accessible to all users of the system that have the proper path in the PYTHONPATH system environment variable. Under Linux however, the problem is exacerbated by the fact that the files themselves may not be created with read and execute access for other users and may need to have their permissions manually modified after installation.
WARNING: urllib vs urllib2 vs urllibx
Both other answers claim that the problem is you're not specifying the correct "version" of the module in the call to pip. Neither is correct, as the error clearly indicates an installation folder access permissions violation causing the failure, but they also incorrectly recommended VERY unsafe behavior.
pip install urllib != pip install urllib5 these are two completely different packages.
The documentation for pip (https://packaging.python.org/tutorials/installing-packages/#id17) clearly says the way to specify a module version explicitly is pip install 'urllib==5'.
As part of how the package management engine implemented by pip works, running the command pip install urllib will always try to use the latest version of the urllib package, so you shouldn't need to specify the version unless you have some reason that you need a very specific version of the module.
There are two points to make in order to answer your question:
1. You are lucky you did not install that package!
The package you were trying to install was a maliciously created python package that was designed to look like a real package (in this case urllib3). If you had installed it, the package would have operated as normal except it would have sent some basic information about the system on which you installed the package to a URL (you can see more details on this here). You can read more about this fake package at either of the following links:
https://app.threatconnect.com/auth/incident/incident.xhtml?incident=5256822&owner=Common%20Community (you can sign up for a free account to view this one)
http://www.nbu.gov.sk/skcsirt-sa-20170909-pypi/index.html
Sending basic information about your systems to an unknown source isn't the worst thing you could do, but is certainly something you want to avoid when possible.
2. To properly install a package...
Specifically urllib:
To install urllib, you need to specify the version of the package you would like to install. For example, pip install urllib3.
Any package in general:
As #Elisabete Coelho suggested, you can use the pip search <package-name> feature to view the available packages. This is not perfect, however, as it may list malicious libraries like the one you were trying to install. A good guideline is that you should follow the installation instructions in a package's documentation closely to avoid any unforeseen issues. This is just an unfortunate necessity of living in a world where people make pretend python packages.
I am working with Scrapy framework to scrap out data from website, but getting the following error in command prompt:
ImportError: cannot import name '_win32stdio'
Traceback is attached as a screenshot.
Kindly revert if require directory structure of my program's directory.
Scrapy can work with Python 3 on windows if you make some minor adjustments:
Copy the _win32stdio and _pollingfile to the appropriate directory under site-packages. Namely, twisted-dir\internet. Download these from https://github.com/twisted/twisted/tree/trunk/twisted/internet
pip install pypiwin32
Granted, this is based on my personal experience. Because the repository will certainly change in the future, readers should beware the age of this answer.
Update: the twisted-win package is no longer required because the appropriate files are now included in the twisted package.
I have gone through the same. I have resolved by updating the twisted package
pip install --upgrade twisted
or
pip uninstall twisted and pip install twisted
get whl of twisted (from below link) according to your os and py version and you are good to go!
https://www.lfd.uci.edu/~gohlke/pythonlibs/#twisted