[Bioc-devel] Unreproducible build error with toppgene on devel branch on netbiolo2

[Kern, Lori]

I'm not sure about the error but to answer your questions:

Q1)  The current cycle of release/devel, Bioc devel will also be on the release version of R (until the fall release when we will start using R-devel in prep for the Spring R release).  It should be the release candidate version of R 4.6 but we will likely update soon to the release version.

Q2) On our current system nebbiolo2, all packages are installed, built, and checked fresh daily.  So there will be a new run on today's report.


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 Nanda, Pariksheet via Bioc-devel <bioc-devel using r-project.org>
Sent: Monday, May 4, 2026 4:40 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Unreproducible build error with toppgene on devel branch on netbiolo2

I get a build error on devel [1] with R version 2026-04-17 r89917 [2] on netbiolo2 but I can't reproduce it locally with up-to-date packages and any of these development R versions:
2026-05-04 r89998
2026-04-20 r89917
2026-04-19 r89916
2026-04-19 r89915

Q1) netbioldo2 R r89917 is a bit old; how often is the devel branch R version updated?

Q2) Do failed package build automatically get re-run until they pass, in case their failures are dependency related?
Or is there a way to trigger a re-run without bumping the package version?
I ask because I wonder if it was a dependency version issue given the original error with several S4Vectors functions in the call trace:

* checking tests ...
  Running $B!F(Btestthat.R$B!G(B
 ERROR
Running the tests in $B!F(Btests/testthat.R$B!G(B failed.
Last 13 lines of output:
    9.   $B('(!(Bmethods::callNextMethod(y, ...)
   10.   $B("(B $B(&(!(Bbase::eval(call, callEnv)
   11.   $B("(B   $B(&(!(Bbase::eval(call, callEnv)
   12.   $B(&(!(BS4Vectors (local) .nextMethod(y, ...)
   13.     $B(&(!(BS4Vectors (local) .local(x, ...)
   14.       $B(&(!(BS4Vectors:::evalqForSubset(subset, x, ...)
   15.         $B(&(!(BS4Vectors:::evalArg(substitute(expr), envir, ..., where = parent.frame())
   16.           $B(&(!(BS4Vectors:::.find_arg_enclos(as.character(expr), where = where)
   17.             $B(&(!(BS4Vectors (local) matched_call(which)
   18.               $B(&(!(Bbase::match.call(...)

  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 169 ]
  Error:
  ! Test failures.
  Execution halted

[1] https://secure-web.cisco.com/1vDwD8rTIO1gtYlcpyt28xtWTsz2gcBB5tiHIBbtIO4hR9aBu5yJCW81kLtpXcJNCwyPucPqNfmqbBw0nFNTNEUGfaPlci7fgGuM8zBlAxKbkmhIxits2DtpzIHFZaGIPiYFcghSgQbAhPOGpreNr2_8L2WtmnWphFyk0wvjccn0_wOoBp-NoZ7AU1kzC1C9E9Qa0O6z9rgE3Ef_LcBpQbbB9paoiCsOl4ijtZmcmZ32NYDiSLxa8yfd-cTaJf1P-P2nig0BosYXJ3wuuf5s7TMubejSQUIwsq_19JAOdud698abMDGprTw-BqW5D1fh0/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.24%2Fbioc-LATEST%2Ftoppgene%2Fnebbiolo2-checksrc.html
[2] I'm not sure what's causing the 3 day mismatch in the date listed before the SVN revision.

Pariksheet
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