Develop Reference

Can't find NVidia cudatoolkit package when creating environment from .yml

Hopefully someone can help me, I've tried to search the internet for a solution, but can't seem to find a solution..
I'm trying to create an environment using conda env create -n deltaconv -f environment.yml and somehow conda I'm getting this response:
[Folder]>conda env create -n deltaconv -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- nvidia::cudatoolkit=11.3
I've just freshly installed Miniconda for the task and the environment looks like this:
channels:
- nvidia
- pytorch
- pyg
dependencies:
- pip=21.2.4
- python=3.9.12
- setuptools=52.0.0
- wheel=0.36.2
- protobuf~=3.19.0
- nvidia::cudatoolkit=11.3
- pytorch::pytorch=1.11.0
- pytorch::torchvision
- pytorch::torchaudio
- pyg::pyg=2.0.4
- pip:
- numpy==1.21.5
- progressbar2==4.0.0
- tensorboard==2.8.0
- jupyter==1.0.0
- openmesh==1.2.1
- h5py==3.6.0
- pytest==7.1.2
- deltaconv==1.0.0
Does anyone know why conda is unable to find cudatoolkit 11.3 from the nvidia channel?

Conda can't install packages from requirements.txt available in conda-forge, although package exists in conda-forge

I added conda-forge to the conda channels:
$ conda config --show channels
channels:
- conda-forge
- defaults
my requirements.txt contains, among others, these lines:
ipython-genutils==0.2.0
jupyter-client==6.1.12
jupyterlab-pygments==0.1.2
appnope==0.1.2
jupyterlab-widgets==1.0.0
data==0.4
prometheus-client==0.11.0
latex==0.7.0
scipy==1.5.4
jupyter-core==4.7.1
jupyter-console==6.4.0
async-generator==1.10
vg==1.10.0
sklearn==0.0
postgis==1.0.4
When I try to create a new environment from this requirements.txt using conda with
conda create --name myenv --file requirements.txt
I get the following errors:
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- ipython-genutils==0.2.0
- jupyter-client==6.1.12
- jupyterlab-pygments==0.1.2
- appnope==0.1.2
- jupyterlab-widgets==1.0.0
- data==0.4
- prometheus-client==0.11.0
- latex==0.7.0
- scipy==1.5.4
- jupyter-core==4.7.1
- jupyter-console==6.4.0
- async-generator==1.10
- vg==1.10.0
- sklearn==0.0
- postgis==1.0.4
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/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.
As you can see, conda-forge is listed under "current channels" and ipython-genutils==0.2.0 is available in conda-forge. However, the package is not found. How can I fix this problem?
I tried both conda config --set channel_priority flexible and ... stable
I run Ubuntu 20.04 LTS, Python 3.10 and Conda 4.12.0

It looks to me like this should have been a requirements.txt to be used by pip. Note that conda packages can have slightly different names than what is available on pypi.
ipython-genutils is not the correct name, looking at the link you have provided, the name of the package is ipython_genutils with an underscore. The same is true for the other packages that you have written with a hyphen. They should all be spelled with an underscore.
That leaves
- sklearn==0.0
- latex==0.7.0
- vg==1.10.0
- scipy==1.5.4
- postgis==1.0.4
- data==0.4
- appnope==0.1.2
sklearn==0.0 seems to be a corrupt line in your file. The package's name is scikit-learn. latex, vg and data are not available on conda channels as far as I can tell. The same goes for scipy==1.5.4, only 1.5.3 and 1.6 are available. postgis only goes back to 2.4.3 on conda-forge , see here, but also seems to be different from what is available on pypi. appnope is a package only available for macOS, see it's description:
Simple package for disabling App Nap on macOS >= 10.9, which can be problematic.
So with that in mind, we can create a yml file that installs from both conda channels and from pip (Changes to your file: replaced - with _, removed appnope, added pip dependency, renamed sklearn to scikit-learn and moved it together with latex, scipy, vg, data, postgis to pip requirements. If you are flexible with scipy==1.5.4, I would advise to change it to scipy==1.5.3 or scipy==1.6.0 and move scipy and sklearn out of the pip installed packages):
name: myenv
dependencies:
- ipython_genutils==0.2.0
- jupyter_client==6.1.12
- jupyterlab_pygments==0.1.2
- jupyterlab_widgets==1.0.0
- prometheus_client==0.11.0
- jupyter_core==4.7.1
- jupyter_console==6.4.0
- async_generator==1.10
- pip
- pip:
- scikit-learn
- latex==0.7.0
- scipy==1.5.4
- vg==1.10.0
- data==0.4.0
- postgis==1.0.4
Save this as environment.yml and then do
conda env create -f environment.yml

conda environment and channels

According to the documentation, if I use
conda env export > file.yml
I am able to share the environment with others. For better cross-platform compatibility, a better way would be:
conda env export --from-history > file.yml
listing only the packages explicitly requested (and not their associated dependencies).
That is what I did, I created a requirement yml file with the second command. Here it is:
name: torch
channels:
- defaults
dependencies:
- python=3.8
- humanize
- nltk
- pandas
- lxml
- numpy
- bs4
- fire
- neptune-client
- tqdm
- pyyaml
- torchaudio
- pytorch
- cudatoolkit=11.3
- torchvision
Among those packages, some were installed from the channel conda-forge: channels seem to be lost in the yaml file.
Indeed, if I try and use that file for cloning the environment (same machine):
conda env create -n torch2 --file=file.yml
I get an error for the packages installed from conda-forge (I explicitly installed from conda-forge only neptune-client and fire):
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- torchaudio
- neptune-client
- fire
However, it seems that channels should be included in the yml. For example, on this github issue page I read:
Currently, conda env export does include channels information.
that closes the issue.
What am I missing?
NOTE: pytorch was installed with
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
from the official web page.

What am I missing?
The docs are wrong - or misleading (at best) when it is communicated that conda env export --from-history exports the channels that packages are installed from, or even any channels at all. This is not the behavior you get, nor is it what I get myself:
$ conda env export | head -n 8
name: smithy
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
$ conda env export --from-history | head -n 8
name: smithy
channels:
- defaults
dependencies:
- mamba
- constructor
- cookiecutter
- conda-build
Note that conda env export does include channel information, but in a highly-pinned way that's almost guaranteed to not work across platforms. So that's not going to work for your use case. I'm not sure if this is a bug or an oversight, but it's clearly not producing the desired result for the user.
Now to offer a (opinionated) recommendation on how to proceed: your best bet is to semi-manually curate an environment YAML file yourself and use that as a single source of truth. It looks like you can use your name: torch ... file a s a starting point, adding in the channels and maybe some other details as you go. Don't forget you can tie an individual package to a channel with the channel::package syntax a la
name: torch
channels:
- defaults
- conda-forge
- torch
dependencies:
- python=3.8
<SNIP>
- pytorch::torchaudio
- pytorch::pytorch
- pytorch::cudatoolkit=11.3
- pytorch::torchvision

How to install fiona 1.6?

I am trying to install fiona=1.6 but I get the following error
conda install fiona=1.6
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/noarch::flask-cors==3.0.7=py_0
- conda-forge/osx-64::blaze==0.11.3=py36_0
- conda-forge/noarch::flask==1.0.2=py_2
failed
PackagesNotFoundError: The following packages are not available from current channels:
- fiona=1.6 -> gdal==1.11.4
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
If I try to install gdal==1.11.4, I get the following
conda install -c conda-forge gdal=1.11.4
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: done
Solving environment: |
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- conda-forge/noarch::flask-cors==3.0.7=py_0
- conda-forge/osx-64::blaze==0.11.3=py36_0
- conda-forge/noarch::flask==1.0.2=py_2
failed
PackagesNotFoundError: The following packages are not available from current channels:
- gdal=1.11.4
Current channels:
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/osx-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/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.
This is the result of conda info
conda info
active environment : base
active env location : /anaconda3
shell level : 1
user config file : /Users/massaro/.condarc
populated config files : /Users/massaro/.condarc
conda version : 4.6.11
conda-build version : 3.17.8
python version : 3.6.8.final.0
base environment : /anaconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /anaconda3/pkgs
/Users/massaro/.conda/pkgs
envs directories : /anaconda3/envs
/Users/massaro/.conda/envs
platform : osx-64
user-agent : conda/4.6.11 requests/2.21.0 CPython/3.6.8 Darwin/17.5.0 OSX/10.13.4
UID:GID : 502:20
netrc file : None

Python Versions
The Conda Forge channel only has gdal v1.11.4 for Python 2.7, 3.4, and 3.5. You either need to use a newer version of Fiona (current is 1.8) or make a new env that includes one of those older Python versions.
For example,
conda create -n fiona_1_6 fiona=1.6 python=3.5
Channel defaults is Required
Another issue you face is that you have removed the defaults channel from your configuration (as per your conda info). It is impossible to install fiona=1.6 with only the conda-forge channel. My recommendation would be to have both conda-forge and defaults in your configuration, but just set conda-forge to have higher priority (if that's what you want). You can do this like so,
conda config --append channels defaults
If you really don't want to include defaults, but just want a temporary workaround, then you can simply run the first command with a --channels | -c flag
conda create -n fiona_1_6 -c conda-forge -c defaults fiona=1.6 python=3.5
This will still give conda-forge precedence, but allow missing dependencies to be sourced from defaults.
Environment File
If you have more than just Fiona that you require, it may be cleaner to put together a requirements file, like so
fiona_1_6.yaml
name: fiona_1_6
channels:
- conda-forge
- defaults
dependencies:
- python=3.5
- fiona=1.6
- osmnx
Then create the new environment with this:
conda env create -f fiona_1_6.yaml

Doing what the error message told me to,
To search for alternate channels that may provide the conda package you're
looking for, navigate to https://anaconda.org
and typing in gdal in the search box led me to https://anaconda.org/conda-forge/gdal which has this installation instruction:
conda install -c conda-forge gdal=1.11.4
Try that to install the gdal dependency, maybe?

Can't install qutip with anaconda in linux

I have the latest anaconda version from linux 32. I'm trying to install qutip with the command
conda install qutip
but the package is missing. I already tried adding conda-forge channel.
Any idea of why the package is missing? According to the Qutip documentacion this should be a possible way to install the package.
Error message:
Fetching package metadata ...........
PackageNotFoundError: Packages missing in current channels:
- qutip
We have searched for the packages in the following channels:
- https://conda.anaconda.org/conda-forge/linux-32
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.continuum.io/pkgs/free/linux-32
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/linux-32
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/linux-32
- https://repo.continuum.io/pkgs/pro/noarch

Indeed, we do not have linux32 builds on conda. You can install via pip though, or build from source.

You need to add a channel to install from that includes your build architecture. The conda-forge channel only has linux-64 builds: https://anaconda.org/search?q=qutip It doesn't look like there are any channels that support linux-32, but you can find the recipe for conda build here: https://github.com/conda-forge/qutip-feedstock, so you might be able to build your own package.