Singularity image with default build template is not working

[maxulysse]

For an nf-core pipeline (rnadnavar), working with @RaqManzano, we created a docker container and a singularity image from this environment.yml (cf nf-core/rnadnavar#78):

channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::bioconductor-complexheatmap=2.26.1
  - bioconda::bioconductor-rtracklayer=1.70.1
  - conda-forge::r-data.table=1.17.8
  - conda-forge::r-dplyr=1.2.1
  - conda-forge::r-ggpubr=0.6.3
  - conda-forge::r-ggrepel=0.9.8

both build without problem, and tests when running well with docker.
Then when we ran tests with singularity, we noticed this error:

Command error:
    During startup - Warning messages:
    1: package 'utils' in options("defaultPackages") was not found
    2: package 'stats' in options("defaultPackages") was not found
    Error: package or namespace load failed for 'stats4':
     .onLoad failed in loadNamespace() for 'utils', details:
      call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
      error: error in running command
    Error: package 'stats4' could not be loaded
    Execution halted

@erikrikarddaniel reported a similar issue on slack https://nextflow.slack.com/archives/C02TLU6K87P/p1782230322495689
@mashehu suggested to rebuild using a different build template, and suggested pixi.

This new singularity image is working as expected and this has solved our issue:

https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/00/0003a3962c416b4c458909d28e343758adf347e614507137b70ac5e4a3c094bb/data

[nictru]

Encountered the same issue and opened an entry on the seqera forum before I saw this. This regression is very annoying

[ewels]

Should be fixed by #1070, I believe.