[Bioc-devel] Package dependencies error during BiocCheck

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.

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}}