[Bioc-devel] Packages with broken setClass statement

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Apr 9 01:17:15 CEST 2019

Dear developers,

Here is another change in recent R devel that affects a few Bioconductor software packages. setClass() used to be tolerant to typos when specifying slot names in the prototype of the class. E.g. this works in R 3.5:

    setClass("A", slots=c(stuff="ANY"), prototype=list(fluff=1:3))

This was certainly not an intended feature. The good news is that in R 3.6, it is now an error:

    setClass("A", slots=c(stuff="ANY"), prototype=list(fluff=1:3))
    # Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  :
    #   The prototype for class "A" has undefined slot(s): 'fluff'

This change breaks the 6 following Bioconductor software packages:

  - Mulcom
  - plateCore
  - proFIA
  - puma
  - TCseq
  - VanillaICE

All these packages seem to have a typo in the supplied prototype of one of their setClass() statement that got unnoticed for years.

If you maintain one of the above package, please fix your package as soon as possible.

Keep in mind that all Bioconductor packages will need to pass 'R CMD build' and 'R CMD check' with no error in order to be included in the next Bioconductor release, scheduled for Tuesday April 30. Note that Bioconductor 3.9 will be based on R 3.6 (scheduled to be released on Friday April 26) so please make sure to use a recent version of R devel when testing/fixing your package.

See our release schedule:


and this recent announcement on this list:


Thanks again you for your ongoing contribution to Bioconductor.



Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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Seattle, WA 98109-1024

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