[Bioc-devel] BiocCheck not available in bioc-devel docker container

[Mike Smith]

Hi Stevie,

It might be helpful to link to the workflow runs so people can see exactly
what you're doing and what's happening.  Hopefully I'm looking in the right
place at https://github.com/steveped/ngsReports/actions/runs

I'm not sure about the error message regarding BiocCheck.  However there
are couple of things I noticed in your workflow files for the most recent
failures, which might help:

In the devel workflow (
https://github.com/steveped/ngsReports/actions/runs/3425103022/) I'm pretty
sure r-lib/actions/setup-r has to be given the version 'devel'.  Using 4.3
won't work because there isn't a URL for R with that version until it
becomes the latest release.

In the latest release workflow run:

   - At line 54 (
   https://github.com/steveped/ngsReports/actions/runs/3426634604/workflow#L54)
   you using the RSPM for Ubuntu Focal and
   - At line 118 (
   https://github.com/steveped/ngsReports/actions/runs/3426634604/workflow#L118)
   you're calling 'remotes::system_requirements("ubuntu", "20.04"))'

but the docker containers are actually built on Ubuntu 22.04, which is
Ubuntu Jammy.  I suspect that's the reason you're getting
the libicui18n.so.66 error, because the binary packages you're installing
are for a different version of Ubuntu.

Also, this might not simplify your workflow too much, but you could try my
setup-bioc action (
https://github.com/grimbough/bioc-actions/tree/v1-branch/setup-bioc) which
tries to make keeping R and Bioconductor versions in sync a bit easier.

Cheers,
Mike


On Wed, 9 Nov 2022 at 04:43, Stevie Pederson <stephen.pederson.au using gmail.com>
wrote:

> Hi,
>
> I also can't get my github actions bioc-check workflow running for devel,
> so I checked the bioc-devel docker image & can't seem to install BiocCheck
> on that container. Is this likely to be available for devel soon? Error
> from my local installation of the container below:
>
>  BiocManager::install("BiocCheck")
> 'getOption("repos")' replaces Bioconductor standard repositories, see
> '?repositories' for details
>
> replacement repositories:
>     CRAN: https://cloud.r-project.org
>
> Bioconductor version 3.17 (BiocManager 1.30.19), R Under development
> (unstable) (2022-11-07 r83308)
> Installing package(s) 'BiocCheck'
> Warning message:
> package ‘BiocCheck’ is not available for Bioconductor version '3.17'
>
> A version of this package for your version of R might be available
> elsewhere,
> see the ideas at
>
> https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
>
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>
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