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

Mike Smith gr|mbough @end|ng |rom gm@||@com
Thu Nov 10 09:34:27 CET 2022

Hi Stevie,

To follow up on this, BiocCheck is missing from devel because some changes
in R-devel tripped up a few unit tests, and the package hasn't been built
successfully.  It looks like Marcel has fixed those issues (
https://code.bioconductor.org/browse/BiocCheck/commits/master) and it
should be available in a day or so once the build system has next run.

I see you also ran into the problem where calling system_requirements("ubuntu",
"22.04") gives an error about not being able to use Ubuntu 22.04.  This is
unfortunate as the fix for this was merged into remotes in April (
https://github.com/r-lib/remotes/pull/705) but that version has never made
it to CRAN!  However, since you're running in the Docker container all of
the system requirements are already installed (that's one of the key
reasons to use the container), so you can actually just remove that step
entirely.  If you ever stop using the container you'd need to reinstate it.


On Wed, 9 Nov 2022 at 12:04, Mike Smith <grimbough using gmail.com> wrote:

> 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
>>         [[alternative HTML version deleted]]
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