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conda install -c bioconda checkv. Is there something I did wrong when I updated the recipe?
So I ran into this trying to update figure out the right workflow for my system
So its clear what I want to do is not the "conda approved" workflow so I am trying to figure out the right method.
I have software repo A that provides a conda environment to run it. Then I have software repo B that uses repo A as a dependency but also adds a number of additional dependencies that are not needed for repo A.
It seems like what I would want is to specify a new environment in repo B that is something like "these dependencies plus whatever is in the repo A environment file" and for the package manager to solve for if that's possible (and it will be) and build me that environment. If its not possible it would throw and error just like it does if I make a single environment file that isn't possible, like asking for specific versions of packages that don't go together.
What is the suggested workflow for this? Would env update second_file.yaml work to add second set of dependencies?
ImportError: libffi.so.7: cannot open shared object file: No such file or directoryI see
libffi.so.6in the system lib64, and
libffi.so.8in my ~/micromamba/lib (it's a symbolic link to somewhere else in the hierarchy). Is this most likely a problem with the conda package?
conda install mist -c jacob-barhak- here is the error I am getting
CondaMultiError: CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/jacob-barhak/win-64/win-64\inspyred-1.0-py27_0.tar.bz2>- can anyone with a windows machine can try to verify this is what they get...
I also tried
conda install inspyred -c jacob-barhak separately - it seems the problem is with this specific package and it is either a conda error or a cloud flare error since there is CF message attached to the http error. Here is how it loos like:
Downloading and Extracting Packages inspyred-1.0 | 78 KB | | 0% CondaMultiError: CondaHTTPError: HTTP 404 NOT FOUND for url <https://conda.anaconda.org/jacob-barhak/win-64/win-64\inspyred-1.0-py27_0.tar.bz2> Elapsed: 00:00.423906 CF-RAY: 74c04c37b9b174a1-LHR An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way.
Is there a way to tell if this is a conda issue or a cloud flare issue?
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hostenvironment during the building phases.
~/.condafor the pkgs and cache, but I don't see a way to force this for the case of root.
condain some user's account, without adding root-owned stuff there... You can define temporary
CONDA_PKGS_DIRS. It might redownload things again, but it shouldn't touch the original pkgs location.
~/.condais out of necessity, I'd say. It doesn't change locations because it knows it's another user's property. It does it because it can't write there. By redefining CONDA_PKGS_DIRS (or adding a
/root/.condarcwith equivalent contents
pkgs_dirs: [your_path]), you are mimicking this process, I think.
continuumio/anaconda3Docker container I try to install the
pyopenmspackage. But the package cannot be found in the
biocondachannel. It is clearly there.
(base) root@61346253da63:/# conda install -c bioconda pyopenms 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: - pyopenms Current channels: - https://conda.anaconda.org/bioconda/linux-aarch64 - https://conda.anaconda.org/bioconda/noarch - https://repo.anaconda.com/pkgs/main/linux-aarch64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-aarch64 - 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.
aarch64, but the package is only built for linux-64 (amd64 aka Intel/AMD). Is this Docker on Apple Silicon? You can use
--platform linux/amd64in your
docker runcommand to use arch emulation for linux-64.
conda-forgeas base channel (not defaults)