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. This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel