[Bioc-devel] Package dependencies error during BiocCheck

Sarvesh Nikumbh @@rve@h@n|kumbh @end|ng |rom gm@||@com
Tue Oct 25 18:27:49 CEST 2022

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
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

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
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

Any leads?

Thanks in advance.


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