Are package downgrades a necessary evil in Conda?

Are package downgrades a necessary evil in Conda?


I am just trying to get my head around using conda environments.

I created a conda environment for a project containing plink2, plink, R and bcftools.

When I installed plink, using mamba install -n autozygosity -c conda-forge plink, I got the output:

  Package         Version  Build               Channel                    Size

  + plink       1.90b6.21  hec16e2b_2          bioconda/linux-64           7MB


  - curl           7.86.0  h7bff187_1          conda-forge
  + curl           7.86.0  h2283fc2_1          conda-forge/linux-64     Cached
  - krb5           1.19.3  h3790be6_0          conda-forge
  + krb5           1.19.3  h08a2579_0          conda-forge/linux-64     Cached
  - libcurl        7.86.0  h7bff187_1          conda-forge
  + libcurl        7.86.0  h2283fc2_1          conda-forge/linux-64     Cached
  - libnghttp2     1.47.0  hdcd2b5c_1          conda-forge
  + libnghttp2     1.47.0  hff17c54_1          conda-forge/linux-64     Cached
  - libssh2        1.10.0  haa6b8db_3          conda-forge
  + libssh2        1.10.0  hf14f497_3          conda-forge/linux-64     Cached
  - python         3.11.0  h582c2e5_0_cpython  conda-forge
  + python         3.11.0  ha86cf86_0_cpython  conda-forge/linux-64     Cached
  - r-openssl       2.0.4  r42hfaab4ff_0       conda-forge
  + r-openssl       2.0.4  r42h1f3e0c5_0       conda-forge/linux-64     Cached


  - openssl        1.1.1s  h166bdaf_0          conda-forge
  + openssl         3.0.7  h166bdaf_0          conda-forge/linux-64     Cached


  - bcftools         1.16  hfe4b78e_1          bioconda
  + bcftools          1.8  h4da6232_3          bioconda/linux-64         794kB
  - htslib           1.16  h6bc39ce_0          bioconda
  + htslib            1.9  h4da6232_3          bioconda/linux-64           1MB


  Install: 1 packages
  Change: 7 packages
  Upgrade: 1 packages
  Downgrade: 2 packages

  Total download: 9MB

This is kind of annoying since I would like to use some of the more recent features in htslib/bcftools and 1.8 is a pretty old version.

Are these kind of downgrades just a necessary part of using conda or is there something to be done? I guess one option is to create a new environment just for plink, but this seems like it could get messy quite quickly!




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