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hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
85 stars 26 forks source link

conda install failure #65

Open jodyhey opened 3 years ago

jodyhey commented 3 years ago

We are trying to install xpclr and several attempts in different environments returns the following (below) Unfortunately details are lacking. Are there particular dependencies ? We can set up a conda environment specifically for xpclr, if we know what needs to be there.

thanks J. Hey

$ conda install -c bioconda xpclr 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 each other:

Output in format: Requested package -> Available versions

hardingnj commented 3 years ago

It may be conflicting with packages already in your environment: perhaps try a new environment, ie:

conda deactivate conda create --name xpclr -c bioconda xpclr

I haven't updated the bioconda in a while though, so very possible it has broken somewhere!

jodyhey commented 3 years ago

Thanks unfortunately that fails as well (below). Any chance of an update?

conda create --name xpclr -c bioconda xpclr Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. |failed

UnsatisfiableError:

hardingnj commented 3 years ago

Build seems ok to me. I can create a new environment containing xpclr. Bioconda checks seem fine too. https://bioconda.github.io/recipes/xpclr/README.html

Can you post the conflicts you are getting?

hardingnj commented 3 years ago

Might be worth posting your conda version too.

jodyhey commented 3 years ago

I posted the text that came back, though it had little info about conflict. Not sure if there is a way to get more details.

I've tried it with conda version 4.8.3 and 4.9.2, both failed.

hardingnj commented 3 years ago

If you leave it to run, it will dump the failed dependencies.

Looks like it's something to do with h5py. I'll take a look- but nothing seems obvious to me currently.

jodyhey commented 3 years ago

so I tried making a new environment a different way, and this worked conda create -c bioconda -c conda-forge -n xpclr xpclr