I tried to install biopython on Linux Mint 19.3. I got an error message; package mkl==2020.0-166 was missing. I was able to downgrade to that version and tried again, but conda still claims the required version is missing. The list output shows: 'mkl [version] 2020.0 [build] 166'. I don't seem to understand how to give biopython the specific version it needs.
I found the question, How do I install biopython in anaconda?
which is closely related. I tried installing from the conda-forge cahnnel without success. Navigator also gave me the same error.
Here is the information about my system and the results I got:
** information pulled because I couldn't format it right.**
Related
There are a lot of other questions like mine but they're quite outdated so I think a new updated guide would be helpful for everyone trying to install rpy2 in Python.
In my case, I'm trying to work with the package pymer4 but i couldn't manage to correctly import it.
I found out that the error lies in rpy2.robjects so I decided to follow this answer to create a clean environment
Steps
I created a new conda environment
conda create -n rpy2_env r-essentials<4.2 r-base<4.2 python=3.7
I set the version to <4.2 because I read online this problem can be caused by a wrong r version. Anyway neither 4.2 nor 4.1 worked for me.
I installed the pymer4 package (and its dependecies, including rpy2)
conda install -c ejolly -c conda-forge pymer4
I downgraded rpy2 to 3.4.5 (see related question below, I also tried without downgrading)
conda install rpy2=3.4.5
When i try to import pymer4 or rpy2.robjects the following error shows up
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) :
3 arguments passed to .Internal(gettext) which requires 2
In the terminal the logs showed no error during download and installation.
If you need more info about my system or anything else, comment and I will update the question.
I am really stuck at this point, I think i tried everything I could. I would really appreciate if someone could enlighten me.
Similar Questions
Import rpy2 : unable to determine R library path
Rpy2 can't find my R libraries on install
R[write to console]: Error in gettext(fmt, domain = domain, trim = trim) : 3 arguments passed to .Internal(gettext) which requires 2
I think I found the solution.
The problem is with conda and rpy2, apparently rpy2 installed with conda is outdated.
You can install correctly rpy2 on a new environment (venv or conda env) using pip.
I did it and so far it's working perfectly.
I'm trying to install a package called pyeto. Their website (https://pyeto.readthedocs.io/en/latest/) does not mention any problems regarding the installation and I can't find any installation related problems of other users. I'm doubting what solution I should look for (I would appreciate it to not have to reinstall python). I'm running python version 3.6.8 and the errors are presented below.
If you have an idea on how to solve this issue please let me know. I'm not an expert on how python runs in the background and how packages are installed through pip. Thanks in advance! B.
ERROR: Could not find a version that satisfies the requirement pyeto (from versions: none)
ERROR: No matching distribution found for pyeto
EDIT: pip --version
pip 20.2.2 from c:\users\user\anaconda3\lib\site-packages\pip (python 3.6)
The author hasn't put it on pypi, so pip is treating it as an unknown package.
See https://github.com/woodcrafty/PyETo/issues/3
Check on the website on what version it is supported.
I am trying to install fiona and geopandas for python on Windows 10 and keep running into an error "ERROR 1: Can't load requested DLL".
I know this question is similar to other questions that have been asked, but I have followed the steps in multiple answers and tutorials and still can't seem to get this to work.
The closest I got was using the steps outlined in this tutorial : https://geoffboeing.com/2014/09/using-geopandas-windows/
and are summarized as follows:
installed the .whl files for rtree, pyproj, shapely, gdal, geopandas, fiona from https://www.lfd.uci.edu/~gohlke/pythonlibs/
Rtree-0.8.3-cp37-cp37m-win_amd64.whl
pyproj-2.2.1-cp37-cp37m-win_amd64.whl
GDAL-3.0.0-cp37-cp37m-win_amd64.whl
geopandas-0.5.0-py2.py3-none-any.whl
Fiona-1.8.6-cp37-cp37m-win_amd64.whl
Shapely-1.6.4.post2-cp37-cp37m-win_amd64.whl
navigated to download folder and used pip install to install GDAL wheel
added the osgeo path to my windows user Path environment variable
used pip install to install remaining wheels (geopandas last), everything installed without errors
As a check, I ran gdalinfo --help-general and get the following output:
This is where I get the "ERROR 1: Can't load requested DLL:" error. It says it cannot find the specified module "ogr_FileGDB.dll". The weird thing is, that .dll is actually in the location that it is looking in???
Also, in python shell, when trying to import fiona or geopandas I get the following errors:
This is beyond my level of troubleshooting...would really appreciate if anyone could get this thing working for me!!!!
FYI - running Python 3.7.3, Windows 10, pip is updated.
Lastly and potentially important (not sure how it plays in?) I already have a GDAL_DATA system variable defined, and also (maybe incorrectly?) also tried adding the osgeo path to my system path variable:
I was using a GDAL version that was not compatible with Fiona and subsequently causing issues with geopandas.
I uninstalled GDAL 3 and installed GDAL 2.4.1 and it worked fine, as cgohlke suggested.
Install fiona with conda, then that will solve the GDAL problem. pip install geopandas should work after that.
I have problems with installing Autokeras with Anaconda.
I downgraded python to 3.6
I installed pytorch and downgraded to
version 0.4.1
I downgraded numpy to 1.14.5
I installed visual studio C++ build tool
But now I get the error that tensorflow will require max numpy version 1.14.5. but autokeras will upgrade numpy to 1.15.4 and it failed to build the wheel for lws
After every step ther was an error.
Is there a simple, straight forward way to install Autokeras on Annaconda (Win)?
Thanks for your help
I have Windows 10, Anaconda 2019.10 and Python 3.7.5. In my case, I get the error ERROR: No matching distribution found for torch==1.0.1.post2 (from autokeras) on Windows 10 when trying to pip install autokeras as indicated by the official documentation.
Then I try to get the source code from https://github.com/keras-team/autokeras and run python setup.py install. It successfully installs autokeras for me.
I had the same issues, using Windows 10 Pro. I installed VMware Workstation 15 Player, installed lubuntu as the guest OS, installed anaconda onto that, created a conda virtual environment, and was able to install autokeras as per https://autokeras.com/start/ . The autokeras installation gave a numpy version error, but seems to work. This might not be the answer you are looking for.
Another answer you might not be looking for is to use Docker, as per https://autokeras.com/docker/ . Once I'd changed "$(pwd)":/app to "$(pwd):/app" in the example, this also seems to work.
I'm trying to install an older version of SciPy (either 0.16.1 or 0.17.0), but when I try to use pip I get the result:
pip install scipy==0.16.1
I get the following message
Failed building wheel for scipy
So I found the .whl file here https://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy but the problem is that the version here is 1.0.1, and I can't seem to find any older ones, even in the SciPy website (there are for linux and mac)
.
.
PS.
I need to use either of this versions because I'm trying to run Theano on a GPU, and the tutorial provided here http://deeplearning.net/software/theano/install_windows.html says this version is a requirement if there is any tutorial that is better and more up-to-date I would be appreciated