[Bioc-devel] Submission #128 (gDRplots): macOS and Windows check runners resolve release, Linux resolves devel

[Kern, Lori]

There is a slight misconception on what release and devel mean in this scenario.  They are not referring to release and devel of Bioconductor, they are referring to the release or devel version of R.  In this current cycle Bioconductor devel is still using  R-release for testing not R-devel (in prep for the new release next year).

I'm looking at your comment on the issue as well,  you reference posit repositories for bioconductor packages but those are not utilized and I'm curious as to why or how you came to that conclusion?   The Bioconductor r-universe repositories are what are being utilized for dependencies and from the detailed looks of the run, it is pulling dependencies from the correct devel r-universe of Bioconductor.

Also,  if your package is needing the higher version of gdrtestdata then that should be changed in your description file as you are also still referencing 1.6.0 version of the package.

It does seem strange that I cannot find gDRtestData in the list of installed packages during the run log; and I'm not finding it in the current Bioconductor universes.   We will follow up on this to find out why and perhaps that will clear the issue.

As far as reviewer assignment: It is an automatic system, so it waits for a clean build for the reviewer to be assigned. There is a way to override it, but let's see if we can get it resolved first by making sure the gDRtestData is available in the universe.  (I would still recommend upping the version needed in the description as that does appear to be inaccurate then) . If that does not help once its available,  we can override and go ahead with assignment while we all investigate the issue.

Cheers,


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Arek G�adki <gladki.arkadiusz using gmail.com>
Sent: Tuesday, September 1, 2026 1:35 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Submission #128 (gDRplots): macOS and Windows check runners resolve release, Linux resolves devel

Hello,

I maintain gDRplots, submitted on 4 August (BiocContributions issue #128).
Two of the three check platforms have been failing since submission, and I
think the cause is on the infrastructure side rather than in my package, so
I'd like to ask about it here.

In a single r-universe run, the runners resolve Bioconductor dependencies
from two different branches:

  linux-release-x86_64    bioconductor.posit.co/packages/devel
gDRtestData 1.11.7   OK
  macos-release-arm64     bioconductor.posit.co/packages/3.23
 gDRtestData 1.10.0   ERROR
  windows-release-x86_64  bioconductor.posit.co/packages/3.23
 gDRtestData 1.10.0   ERROR

My examples use a directory that was added to gDRtestData during the
current devel cycle, so system.file() finds it on Linux and returns "" on
macOS and Windows. That single difference is the only ERROR left on either
platform.

Is this intentional? It doesn't look specific to gDRplots � any submission
depending on something added to a Bioconductor package during the current
cycle would fail on exactly those two platforms and pass on the third.

And a related question I genuinely don't know the answer to: is a clean
build on all platforms a precondition for a reviewer being assigned, or can
review start in parallel? My submission has been in pre-review for four
weeks and I'd like to know whether I'm waiting on this or on something else.

I do have a local workaround � guarding the affected examples so they skip
when the data isn't installed � but I'd rather not push it if the runners
are meant to resolve devel, since it would just hide the difference.

Thanks,
Arek Gladki

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