I need to update cartopy 0.16 to 0.17 because of this bug fix.
bash command conda list | grep cartopy returns:
cartopy 0.16.0
When I then do conda update cartopy
I get:
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
But then checking again, I still have cartopy 0.16.
I've also tried the commands:
conda install -c conda-forge cartopy (that just installs 0.16) and conda install cartopy=0.17 which takes me through a long list of returns that starts with this:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Examining conflict for conda basemap scipy python mkl_fft twyt...
But it ultimately doesn't update cartopy.
Does anybody know how I can get the new version with conda?
It looks like there are packages in your current env that are conflicting with the newer version of cartopy. I suggest creating a seperate environment for that cartopy version:
conda create -n <someName> python=<your desired version> cartopy=0.17 <other packages you may need>
Related
I tried to install optitype as follow:
conda install -c bioconda optitype
I got the message:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
optitype -> python[version='2.7.|>=2.7,<2.8.0a0|3.5.|3.4.*']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with your system:
feature:/linux-64::__glibc==2.31=0
feature:|#/linux-64::__glibc==2.31=0
Your installed version is: 2.31
So, I tried to install python 2.7 in conda:
conda install -c anaconda python=2.7
which gave me hundred of conflicts and finished by saying that I installed:
Your installed version is: 2.31
I re-tried to install optitype but it's not working!
If someone has an idea!
Bioconda as a channel builds atop the conda-forge channel. Any specification that does not prioritize that (such as prioritizing anaconda channel) is incorrect. Also, do not bother changing Python versions in-place beyond patches - nearly every package will have to be reinstalled, such that it is much more simple for the solver to create a new environment. Try something like,
# name the environment something meaningful (not "foo")
conda create -n foo -c conda-forge -c bioconda python=2.7 optitype
Feel free to include additional packages that you require in the same line.
Note that mamba is much faster than conda, especially when solving for older packages like this. That is, were I installing this, I would use:
# install mamba if not already installed
conda install -n base -conda-forge mamba
mamba create -n foo -c conda-forge -c bioconda python=2.7 optitype
I am trying to run a python code in PyCharm that requires cartopy. Cartopy will not install on my Anaconda 3. My computer is running Windows. I have tried entering the following in Anaconda 3 and get the error:
(base) PS C:\Users\w______> conda install -c conda-forge/label/cf201901 cartopy
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Please help! Is there another way I can install cartopy? My maps are due next week and nobody at the university seems to be able to help me.
I am getting the following error output when trying to install eomaps using Conda. I don't know how to solve this. I have also tried the same using pip but it didn't seem to solve the problem. Here is the error that Conda reports:
(base) C:\Windows\system32>conda install -c conda-forge eomaps
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Here is the error that pip reports:
ERROR: Failed building wheel for cartopy
ERROR: Command errored out with exit status 1:
------
ERROR: Failed building wheel for fiona
ERROR: Could not build wheels for cartopy which use PEP 517 and cannot be installed directly
How can I get this to install?
EOmaps dev here...
I think the problem is that you're installing packages in your (base) environment! You most probably have some packages installed (previous versions of cartopy, pyproj etc.?) that conflict with the requirements of EOmaps which is why the conda-solver does not succeed.
I'd strongly suggest working in a fresh environment and NOT in the base environment!
(Checkout conda user-guide - managing environments)
As an example, the following should work without any problems:
conda create -n eomaps_env python=3.9
conda activate eomaps_env
conda install -c conda-forge eomaps
(the name eomaps_env and the python-version are both optional and you can change it to whatever name and version you like!)
To speed up solving complex dependencies you can also try to use mamba (a c++ reimplementation of the conda package manager) which does the very same thing as conda (but solving dependencies works a lot faster):
conda create -n eomaps_env python=3.9
conda activate eomaps_env
conda install -c conda-forge mamba
mamba install -c conda-forge eomaps
My Conda Environments are not showing up in my Jupiter Notebooks. I've reviewed all the (excellent) dialogue here, but it doesn't appear to work for python 3.9.2.
I tried the following, which didn't work:
conda install jupyter
conda install ipykernel
conda install nb_conda
Then when I try the following conda install nb_conda_kernels I get the following error:
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- nb_conda_kernels -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
Your python: python=3.9
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
How can I get my conda environments to show in jupyter notebooks in python 3.9.2? Thank you!
Try using the conda-forge channel, e.g.:
$ conda install -c conda-forge ipykernel
And you don't need to install jupyter if this conda env is just a kernel to add, if that's what you want to do.
After that, you need to run this in that conda env:
$ python -m ipykernel install --user --name vanilla --display-name "Python 3 (vanilla)"
Replace the name and display-name to your liking.
I am new here and also just learning how to work in anaconda, so I would like to ask for help. I need some packages installed to be able to run my sequence analysis and calculate dN/dS ratio. For that I need paml, clustal omega, prank, blast and pal2nal packages to be installed. I'm working in Windows 10 (unfortunately, but no other way - working laptop).
I have been trying to install pal2nal package in anaconda using conda, bioconda, pip commands and I always get the same error.
My tries: conda install -c bioconda pal2nal, conda install -c anaconda pal2nal, conda install pal2nal, pip install pal2nal (it doesn't exist among python packages) and I even tried to create a new environment and install it there but no luck. It's the same with the rest of the packages.
The message what I always get is:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError:
Does anyone know why I always get this error and maybe what to do to be able to install these packages?
Thank you very much for help!!
Sorry, but that package is only available through Bioconda and Bioconda does not support Windows natively.
Instead, you will need to work with a virtualization or containerization layer such as WSL or Docker/Singularity.