superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
4 stars 2 forks source link

conda.... #319

Open kevinkle opened 6 years ago

kevinkle commented 6 years ago

Recently this started happening on our CI:

$ if [ "$TO_TEST" = "CONDA" ]; then wget https://raw.githubusercontent.com/superphy/docker-flask-conda/$ENV_BRANCH/app/environment.yml; conda env create -q -f environment.yml -n backend; source activate backend; wget https://raw.githubusercontent.com/superphy/docker-flask-conda/webserver/app/environment.yml -O environment-webserver.yml; conda env update -q -f environment-webserver.yml; wget https://raw.githubusercontent.com/superphy/docker-flask-conda/$ENV_BRANCH/app/requirements.txt; pip install -r requirements.txt; fi
--2018-06-22 20:20:39--  https://raw.githubusercontent.com/superphy/docker-flask-conda/master/app/environment.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 5405 (5.3K) [text/plain]
Saving to: ‘environment.yml’
100%[======================================>] 5,405       --.-K/s   in 0s      
2018-06-22 20:20:39 (85.5 MB/s) - ‘environment.yml’ saved [5405/5405]
Solving environment: ...working... failed
ResolvePackageNotFound: 
  - r-msm==1.6.4=r3.3.2_0
  - tbb==4.4_20150728=0
  - r-phytools==0.6_00=r3.3.2_0
  - r-phangorn==2.2.0=r3.3.2_0
  - r-plotrix==3.6_5=r3.3.2_0
Could not find conda environment: backend
You can list all discoverable environments with `conda info --envs`.

We're still fine since we save everything to Docker images, but we really should move away from conda.