PackageNotFoundError

[YYasmina]

Hello, I tried to use your conda environment and I have this error, did you change anything in the Conda environment?

Fetching package metadata ........... Solving package specifications:

PackageNotFoundError: Packages missing in current channels:

• cibersort -> bioconductor-preprocesscore 1.40.0.*
• cibersort -> openjdk 8.0.144.*
• cibersort -> r-colorramps 2.3.*

We have searched for the packages in the following channels:

• https://conda.anaconda.org/vacation/linux-64
• https://conda.anaconda.org/vacation/noarch
• https://repo.continuum.io/pkgs/free/linux-64
• https://repo.continuum.io/pkgs/free/noarch
• https://repo.continuum.io/pkgs/r/linux-64
• https://repo.continuum.io/pkgs/r/noarch
• https://repo.continuum.io/pkgs/pro/linux-64
• https://repo.continuum.io/pkgs/pro/noarch

Thank you for your helpful code !

[jason-weirather]

Hi @YYasmina , I used this package two days ago and I successfully built the docker on Mac os X, and had no problem executing through the command line via docker. This would have involved constructing this Conda environment in a linux docker. How are you loading the conda environment, what operating system? My main guess at whats going on is you are missing one of the conda channel dependencies, sorry its kind of buried in the README but you need the channels listed in this projects .condarc file. Those are:

channels:
 - vacation
 - conda-forge
 - bioconda
 - defaults

So my guess from what you are missing is that you are failing to get bioconductor from bioconda, and failing to get some of the others from conda-forge.

I think you can put that .condarc in your home directory, or in the root of your environment (i've never tried the later).

If using that .condarc doesn't help please let me know and I'll try to reproduce your error on whatever OS you are having problems on.

Thanks!