How can I install specific Bioconductor package versions using a conda yaml file?

Question

I'm trying to install specific versions of Bioconductor packages using conda. I'm creating a conda environment using a .yml file like this: conda env create -f coo_environment.yml

When I do this, I get:

Collecting package metadata: done
Solving environment: failed

ResolvePackageNotFound: 
  - bioconductor-complexheatmap=2.12.1
  - bioconductor-rtracklayer=1.56.1
  - bioconductor-exomecopy=1.42.0

The relevant contents of coo_environment.yml are shown below

name: coo

channels:
        - conda-forge
        - bioconda
dependencies:
        # R
        - bioconductor-exomeCopy=1.42.0
        - bioconductor-rtracklayer=1.56.1
        - bioconductor-ComplexHeatmap=2.12.1

When I remove the package versions from the yml file, it works. I double checked the versions of the packages here , here , and here , and I believe they're correct.

Answer 1

Bioconda has fallen behind the release cycle of Bioconductor , primarily due to upstream delays of Conda Forge adding R 4.2 and corresponding package builds. Bioconductor tightly couples releases to R versions, such that all the v3.15 package releases depends on R 4.2. Conda Forge has recently started building R 4.2 , however, it has not started migrating the many CRAN packages it hosts, which is a crucial prerequisite. Only with that in place can Bioconda start building the v3.15 versions of Bioconductor packages.

In summary, you cannot rely on the Bioconductor site to identify versions available through Conda. Instead, consult either the Bioconda package index , Anaconda Cloud , or search directly from the commandline, eg,

$ mamba search bioconda::bioconductor-exomecopy
# Name                       Version           Build  Channel             
bioconductor-exomecopy          1.22.0        r3.3.2_0  bioconda            
bioconductor-exomecopy          1.22.0        r3.4.1_0  bioconda            
bioconductor-exomecopy          1.24.0        r3.4.1_0  bioconda            
bioconductor-exomecopy          1.26.0  r341h470a237_0  bioconda            
bioconductor-exomecopy          1.26.0  r351h470a237_0  bioconda            
bioconductor-exomecopy          1.28.0  r351h1de35cc_0  bioconda            
bioconductor-exomecopy          1.30.0   r36h01d97ff_1  bioconda            
bioconductor-exomecopy          1.32.0   r36h01d97ff_0  bioconda            
bioconductor-exomecopy          1.34.0   r40h8909d69_0  bioconda            
bioconductor-exomecopy          1.36.0   r40h68a2ddb_1  bioconda            
bioconductor-exomecopy          1.36.0   r40h8909d69_0  bioconda            
bioconductor-exomecopy          1.38.0   r41h68a2ddb_0  bioconda            
bioconductor-exomecopy          1.40.0   r41h68a2ddb_0  bioconda            
bioconductor-exomecopy          1.40.0   r41haba8685_1  bioconda   

For now, Conda R users can use at latest Bioconductor 3.14, which is tied to R 4.1.