[Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

[Elizabeth Purdom]

Hello,

Our package clusterExperiment has suddenly started producing errors in the bioconductor devel branch because our unit tests are failing, even though we haven’t pushed any changes and they passed previously. We first noticed this on April 5th. 

I believe the source of these errors likely do to calls to SummarizedExperiment() creating the following messages due to conflicts in ‘RNeXML’ and ’S4Vectors’ both defining class ‘Annotated':

> Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
> Also defined by ‘RNeXML’
This is killing a vast number of our tests where we repeatedly use ‘expect_silent’ calls in our unit tests and SummarizedExperiment calls underlie everything.

We had this message issue two years ago (https://github.com/epurdom/clusterExperiment/issues/66), when it appeared to be a problem with two definitions of the ‘Annotated’ class in two packages that are both dependencies of packages we call. At that time, Michael Lawrence posted that he would fix the problem, and it was then fixed in later versions of bioconductor/R. But it appears to be back.  I am unfortunately unable to get the RNeXML package to compile from source on my computer with the current Mac OS X development binary which I just downloaded (2018-04-05 r74542), so I haven’t been able to completely redo the code that we presented in that earlier github issue to confirm it is the exact same problem. I am having to rely on the error reports/logs from both Bioconductor and TravisCI (e.g. 2018-04-07 r74551), where this message shows up everywhere and didn’t before. Thus I’m guessing that since they are the same messages from before that the source is again the call to SummarizedExperiment. 

I would note that in development version 2018-03-22 r74446, where I was able to install all of the packages, I was not getting these messages. 

Thanks,
Elizabeth Purdom
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