[Bioc-devel] Package dependencies error during BiocCheck

[Sarvesh Nikumbh]

Hi Marcel,

Thanks for the reply.

Is there a way to opt for this solution on the bioc new pkg build systems?

If not, then, I guess, I will have to wait until it goes away for my bioc
submission to be reviewed further?

Thanks and best,
  Sarvesh


On Tue, 25 Oct 2022, 18:14 Marcel Ramos, <marcel.ramosperez using roswellpark.org>
wrote:

> Hi Sarvesh,
>
> The error has something to do with an interaction between internal base
> R code
> and checking for dependencies in BiocCheck with `loadNamespace`.
> Either way, this check in BiocCheck is redundant with R CMD check.
> It will soon get removed but for now, you can disable it by running:
>
> BiocCheck("./seqArchRplus", `no-check-dependencies` = TRUE)
>
> Best,
>
> Marcel
>
>
> On 10/25/22 12:27 PM, Sarvesh Nikumbh wrote:
> > Hi all,
> >
> > I am trying to resolve an issue with dependencies of my package which is
> > under review at the moment (Issue 2790
> > <https://github.com/Bioconductor/Contributions/issues/2790>, latest
> report
> > <
> http://bioconductor.org/spb_reports/seqArchRplus_buildreport_20221025084934.html
> >).
> > I was wondering if somebody else also encountered this issue (see details
> > below), and were successful resolving it. Any help in this regard would
> be
> > greatly appreciated.
> >
> > *The issue:*
> > Running BiocCheck throws the following error:
> >
> > Error in completeSubclasses(classDef2, class1, obj, where) :
> >    trying to get slot "subclasses" from an object of a basic class
> > ("NULL") with no slots
> > Error: .onLoad failed in loadNamespace() for 'dbplyr', details:
> >    call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
> >    error: error in contained classes ("character") for class ident;
> > class definition removed from dbplyr
> > Execution halted
> >
> > which going by info at
> > tidyverse/dbplyr#779<https://github.com/tidyverse/dbplyr/issues/779>  is
> > caused by Brobdingnag<https://github.com/RobinHankin/Brobdingnag>, and
> > resolved with version 1.2-9, which is now also available on CRAN (see
> here
> > <https://github.com/RobinHankin/Brobdingnag/issues/24>).
> >
> > I saw this error earlier on my debian machine only using bioc-devel.
> Here,
> > I could resolve this by re-installing Matrix, dbplyr and Brobdingnag.
> >
> > On bioc-side, the error can be seen on Ubuntu (latest report
> > <
> http://bioconductor.org/spb_reports/seqArchRplus_buildreport_20221025084934.html
> >).
> > Maybe, it would occur on other OSs as well, but that stage is not
> reached.
> > Thanks to Lori and Jennifer from bioc-team, the same re-installation
> > solution was attempted, but this did not resolve it there.
> >
> > Since I do not have access to a machine running Ubuntu around, I have set
> > up GHA. There, interestingly, the same error is encountered on macOS and
> > Windows, but not on Ubuntu -- details here
> > <
> https://github.com/snikumbh/seqArchRplus/actions/runs/3322212068/jobs/5490915503
> >
> > .
> >
> >
> > Any leads?
> >
> > Thanks in advance.
>
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>
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