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

Nanda, Pariksheet PAN79 @end|ng |rom p|tt@edu
Mon May 4 22:40:58 CEST 2026


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 ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.   ├─methods::callNextMethod(y, ...)
   10.   │ └─base::eval(call, callEnv)
   11.   │   └─base::eval(call, callEnv)
   12.   └─S4Vectors (local) .nextMethod(y, ...)
   13.     └─S4Vectors (local) .local(x, ...)
   14.       └─S4Vectors:::evalqForSubset(subset, x, ...)
   15.         └─S4Vectors:::evalArg(substitute(expr), envir, ..., where = parent.frame())
   16.           └─S4Vectors:::.find_arg_enclos(as.character(expr), where = where)
   17.             └─S4Vectors (local) matched_call(which)
   18.               └─base::match.call(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 169 ]
  Error:
  ! Test failures.
  Execution halted

[1] https://bioconductor.org/checkResults/3.24/bioc-LATEST/toppgene/nebbiolo2-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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