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

Mike Smith gr|mbough @end|ng |rom gm@||@com
Wed Nov 9 12:04:10 CET 2022

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 (
   you using the RSPM for Ubuntu Focal and
   - At line 118 (
   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.


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

> 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
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list