[Bioc-devel] Package dependencies error during BiocCheck

Marcel Ramos m@rce|@r@mo@perez @end|ng |rom ro@we||p@rk@org
Tue Oct 25 19:10:04 CEST 2022

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)



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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