I am trying to install qiime1 environment using terminal on Mac. Currently getting an error saying packages not found for matplotlib 1.4.3.
I struggled with the same issue, matplotlib 1.4.3 package not found, and subsequently tried many different solutions, pip install and so on. So I am posting the solution that worked for me, I cannot remember where I found the different suggestions, but the downgrade of conda was key to make it work (thanks to whomever it was that suggested it in the first place):
conda config --set allow_conda_downgrades true
conda install conda=4.6.14
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
print_qiime_config.py -t
Once you've installed qiime you can upgrade your conda to the most recent version if you like
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I installed the geopandas package through anaconda using conda install -c conda-forge geopandas , but for some reason the 0.6.3 version got installed.
I need to use the missing_kwds function, but this function is only available in the latest versions of geopandas (currently it's 0.10.0).
I tried updating it by checking conda install -c conda-forge geopandas -h and then using the ---update-all but after hours of waiting I figured that wasn't right.
Does anyone know how to help me?
You can specify the version number you want to install (example below).
conda install -c conda-forge geopandas=0.10
If you're working in a conda env (which I would highly advise, along with running the 2 conda config steps on the conda-forge home page on your machine to add the conda-forge channel and prioritize installing packages from the conda-forge channel), make sure you've already activated your env before running that install command.
I got something weird on Windows (I don't use it since 2012). I created a conda env long time ago with tensorflow 2.2.0. Now, I want to update tensorflow to the latest. As in Linux, I activate the env and I run pip install tensorflow. The problem that pip installs it in the global package, not in the env.
Here are some logs:
here when I try to uninstall tensorflow 2.2.0. It does not detect it and it detects 2.3.1 which is installed in global package
I think the problem is coming from pip path:
I checked and I see that pip install everything here c:\programdata\anaconda3\lib\site-packages
I tried to create a new environment but I got the same results!!
Anyone got already this problem?
I am a Python Noob. (Using Mac OS 10.12 & Python 3.7)
I'm trying to use mpl_toolkits.basemap
to execute the code
from mpl_toolkits.basemap import Basemap
I googled the way to get matplotlib and successfully installed it.
However, while it's possible to run "from mpl_toolkits.basemap import Basemap" in terminal on mac,
it fails to be loaded if I run the command within IDLE.
Then, I googled to figure out the issue and got the hint that
it could be resolved if I install Basemap properly.
To install Basemap, I think I need to go with "FINK".
However, Fink is only available up to 10.5 OS while mine is 10.12.
And FINK website says do not update OS before upgrading FINK.
However, it's too late for me.
Cause I updated my OS longtime ago and recently I started to learn Python Using Mac.
So I guess, if there is a way to install Basemap not using apt-get,
(the codes below is from "Python basemap module impossible to import")
sudo apt-get install libgeos-3.5.0
sudo apt-get install libgeos-dev
sudo pip install https://github.com/matplotlib/basemap/archive/master.zip
I think my issue could be cleared.
Since I'm really really noob, I'm not sure this is the reason for my failing in "from mpl_toolkits.basemap import Basemap".
What I tried so far is
1) brew install basemap
with the error of
Error: No available formula with the name "basemap"
==> Searching for a previously deleted formula (in the last month)... Warning: homebrew/core is shallow clone. To get complete history run:
git -C "$(brew --repo homebrew/core)" fetch --unshallow
2) pip install basemap
with the error of
Requirement already satisfied
3) sudo pip install https://github.com/matplotlib/basemap/archive/master.zip
with the error of
Command "python setup.py egg_info" failed with error code 1 in
/private/tmp/pip-install-lux494o4/pyproj/
4) conda install basemap
with the following message of
All requested packages already installed.
5) conda install -c conda-forge basemap
with the following message
Preparing transaction: done Verifying transaction: done Executing
transaction: done
Can anyone help to install basemap properly so that I could run
"from mpl_toolkits.basemap import Basemap"
in my IDLe?
My IDLE Sheel keeps saying
Traceback (most recent call last): File "", line 1, in
from mpl_toolkits.basemap import Basemap ModuleNotFoundError: No module named 'mpl_toolkits.basemap'
while my terminal doesn't have problem with running the code.
Appreciate it in advance.
any luck? I spent the day battling this as well. I had the most success when I tried downloading an older version of basemap.
I was using python 2.7 and this worked okay sudo -H pip2 install https://github.com/matplotlib/basemap/archive/v1.1.0.tar.gz
For python 3 try replacing pip2 with pip3 or pip.
Ran into this myself today my solution:
install libgeos on mac
brew install geos
then as you suggested use pip to install mpl_tools:
pip3 install -q https://github.com/matplotlib/basemap/archive/master.zip
This also may help:
missing libgeos_c.so on OSX
Firstly, I suggest you to set Anaconda up. Then follow below steps;
Create a new environment in anaconda.
Install Jupyter Notebook and launch it. If it works, turn it off.
Change your anaconda environment in your terminal.
Try installation commands below;
conda install ...
conda install forge ...
pip install ...
I just installed basemap using
conda install -c conda-forge basemap=1.0.8.dev0
and
conda install -c conda-forge basemap
in the Anaconda prompt but after that I was not able to launch neither Spyder nor Anaconda Navigator. I tried all trick provided here in Stackoverflow but none of them working. Any advice?
Shall I re-install the entire Anaconda without loss my libraries and packages?
(Spyder maintainer here) Mixing conda-forge and default packages is a really bad idea because they are compiled differently. That's the root cause of the problem you're experiencing here.
Shall I re-install the entire Anaconda without loss my libraries and packages?
Yes, I'm afraid you have to do that because you have corrupted your installation.
Any advice?
The solution is to create a separate conda environment to install conda-forge packages, like this
conda create -n basemap-env
source activate basemap-env
conda install -c conda-forge basemap=1.0.8.dev0 spyder
and start Spyder from that environment.
I've been trying to install cvxopt on Anaconda Python 3.x for a while now, reading past posts and I can't seem to make it work. Here is what I have tried so far:
pip install cvxopt --user
which gave me the following error:
Failed building wheel for cvxopt
Then I tried this:
conda install -c omnia cvxopt
output:
UnsatisfiableError: The following specifications were found to be in conflict:
- cvxopt
- python 3.5*
I installed mkl using this:
conda install mkl
which worked but trying out the previous commands still don't work.
I have installed multiple things in the past using the command prompt but my experience has told me to make sure I know and understand what I am installing because I wrecked my computer one time. So instead of trying things blindly, I would like to know if someone had a tipp.
As you can see here cvxopt does not support python 3.5+ due to compiler incompatibility.
Nevertheless, as stated in the comments, you can use anacodna to create a virtual environment and install it.
conda create --name py34 python=3.4 numpy
activate py34
conda install -c omnia cvxopt