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
Related
I have installed Anaconda from scratch and then installed pyomo, which worked.
When I try to install pyomo.extra, it runs about 1/2 hour and then fails.
I had tried:
conda install -c conda-forge pyomo.extras
conda install -c "conda-forge/label/cf201901" pyomo.extras
conda install -c "conda-forge/label/cf202003" pyomo.extras
as recommended on https://anaconda.org/conda-forge/pyomo.extras
and also
conda config --add channels conda-forge
conda install pyomo.extras
subsequently checking with
conda search pyomo.extras --channel conda-forge
as recommended on https://github.com/conda-forge/pyomo.extras-feedstock
indicated that pyomo.extra isn't installed.
here is the generated output.
(base) PS C:\WINDOWS\system32> conda install pyomo.extras
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 pyomo.extras: 75%|███████████████████████████████████▎ | 3/4 [00:03<00:01, 1.15s/it]\failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- pyomo.extras -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|3.4.*']
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.
The following specifications were found to be incompatible with your system:
- feature:/win-64::__win==0=0
- feature:|#/win-64::__win==0=0
- pyomo.extras -> ipython -> __osx
- pyomo.extras -> ipython -> __win
Your installed version is: 0
(base) PS C:\WINDOWS\system32> conda search pyomo.extras --channel conda-forge
Loading channels: -
(base) PS C:\WINDOWS\system32>
Questions:
what might be the reason why installation of pyomo.extra fails?
what alternatives for installing pyomo.extra can be recommende?
The package is only available for Python 2.7, 3.6, and 3.7, but your target environment currently has Python 3.9. Conda will not change the Python version in-place because it entails changing pretty much every package in the environment. Instead, try creating a new environment with a compatible Python version.
## include any other packages now
conda create --name foo python=3.7 pyomo pyomo.extras
Why only old versions? The feedstock repository has been failing to build updated versions since Python 3.8 and no maintainers have stepped in to fix it. If you would like to see updated versions built, then drop an Issue on the feedstock or, if you feel comfortable trying to fix it, send a Pull Request. The squeaky wheel get's the grease!
I think I have an environment problem with miniconda. Here is what I succeded(o)/mismanaged(x) to install python mayavi package.
The documentation writes to type :
(o) conda install vtk
(x) conda install pyqt=4
<(x) conda install mayavi> (not performed)
The output message for another cmd (conda install -c anaconda -c conda-forge mayavi) are:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
I understand that I must check the first failed package: pyqt. There are similar messages, before the shell windows simply breaks. I have read that an updated environment could work but my OS (fedora35 as virtual machine) and python 3.9 + miniconda3 are fast from best versions. Any suggestion or help to fix this or trying docker are welcome
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
I am try ing to install symfit on a MacBook Pro M1 using miniforge, for processor compatibility as pip3 install symfit results into errors. However, when running conda install -c conda-forge symfit, I get:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- symfit
Current channels:
- https://conda.anaconda.org/conda-forge/osx-arm64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/conda/osx-arm64
- https://conda.anaconda.org/conda/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
When doing so, I find that symfit is available in the conda-forge channel! Why can't it be installed from the command line?
At the time of the question, the Conda Forge feedstock for symfit was not building for osx-arm64 platform. After an issue being filed on the feedstock, one of the maintainers updated the feedstock to generate noarch builds (platform agnostic). So, starting with version 0.5.3, what OP attempted should just work.
conda install -c conda-forge symfit
The lesson here is: Conda Forge is an open platform, so if you find something not being built, please reach out to the feedstocks or submit a Pull Request. The community depends on active feedback from users to improve.
UPDATE:
this answer was posted before OP changed to use the correct conda install -c conda-forge symfit command!
turns out at the time of question symfit has no build for "OSX_arm64" which is why the command fails
because conda install will try to install the module from the default channel...
you have to explicitly tell conda to use conda-forge!
conda install -c conda-forge symfit
-> check the doc!! https://symfit.readthedocs.io/en/stable/installation.html
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.