[Bioc-devel] package check failures on machines due to unavailable dependency

[Andres Wokaty]

Hi Mengyuan,

Regarding cellxgene.census, which I see is in the chanzuckerberg r-universe, Bioconductor's current policy states that dependencies should come from either Bioconductor or CRAN as noted at https://contributions.bioconductor.org/description.html?q=depend#depends-imports-suggests-enhances. Alternative approaches are being evaluated but at this time the policy hasn't changed.

Andres Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Mengyuan Shen via Bioc-devel <bioc-devel using r-project.org>
Sent: Thursday, August 27, 2026 12:22 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] package check failures on machines due to unavailable dependency

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Dear Bioconductor team,

I am the maintainer of package cellNexus. I am contacting you about the following error:

cellnexus is currently failing checks on nebbiolo2 and lconway because the suggested dependency cellxgene.census<https://urldefense.com/v3/__https://chanzuckerberg.r-universe.dev/cellxgene.census*readme__;Iw!!LRXxDv2l!XMopwWnHmwrb0nkFtahvcsgg2-h1fzUOdotkb7SMVBRyc2xXU7onNKe_38Teez5d4WY54asgPQkhZ9GmSR_d_s7-XCV2lYRQtA$ > is not available.

`Package suggested but not available: ‘cellxgene.census’`

I have tried removing it from DESCRIPTION Suggests, but it had another check warning, so decided to keep it in Suggests
❯ checking dependencies in R code ... WARNING
  '::' or ':::' import not declared from: ‘cellxgene.census’
  'loadNamespace' or 'requireNamespace' call not declared from: ‘cellxgene.census’

I fixed this in the GitHub CI by conditionally skipping suggested dependencies on windows os as below:

steps:
conditionally skip suggest dependencies for windows os
    - name: Set Windows env vars
      if: runner.os == 'Windows'
      run: echo "_R_CHECK_FORCE_SUGGESTS_=false" >> $env:GITHUB_ENV

What would be the recommended approach for dealing with the check failures? Is this something that can be addressed separately from the package?

Kind regards,
Mengyuan

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