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

[Elizabeth Purdom]

Just to follow up on my previous post. I am able to replicate the problem in the problem like in the github post from 2 years ago (https://github.com/epurdom/clusterExperiment/issues/66 <https://github.com/epurdom/clusterExperiment/issues/66>) only now it is not the SummarizedExperiment class but the SingleCellExperiment class that has the problem. [And I was incorrect, the problem does occur in  development version 2018-03-22 r74446]. 

So this is actually a problem with the SingleCellExperiment package — sorry for the incorrect subject line.

All of the best,
Elizabeth

> > library(SingleCellExperiment)
> > SingleCellExperiment()
> class: SingleCellExperiment 
> dim: 0 0 
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):
> reducedDimNames(0):
> spikeNames(0):
> > library(RNeXML)
> Loading required package: ape
> > 
> > SingleCellExperiment()
> Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
> Also defined by ‘RNeXML’
> Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
> Also defined by ‘RNeXML’
> class: SingleCellExperiment 
> dim: 0 0 
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):
> reducedDimNames(0):
> spikeNames(0):




> > sessionInfo()
> R Under development (unstable) (2018-03-22 r74446)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
>  [1] RNeXML_2.0.8                ape_5.1                     SingleCellExperiment_1.1.2 
>  [4] SummarizedExperiment_1.9.16 DelayedArray_0.5.30         BiocParallel_1.13.3        
>  [7] matrixStats_0.53.1          Biobase_2.39.2              GenomicRanges_1.31.23      
> [10] GenomeInfoDb_1.15.5         IRanges_2.13.28             S4Vectors_0.17.41          
> [13] BiocGenerics_0.25.3        
> 
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.16           pillar_1.2.1           bindr_0.1.1            compiler_3.5.0        
>  [5] plyr_1.8.4             XVector_0.19.9         iterators_1.0.9        bitops_1.0-6          
>  [9] tools_3.5.0            zlibbioc_1.25.0        uuid_0.1-2             tibble_1.4.2          
> [13] jsonlite_1.5           nlme_3.1-137           lattice_0.20-35        pkgconfig_2.0.1       
> [17] rlang_0.2.0            Matrix_1.2-14          foreach_1.4.4          crul_0.5.2            
> [21] curl_3.2               bindrcpp_0.2.2         GenomeInfoDbData_1.1.0 dplyr_0.7.4           
> [25] httr_1.3.1             stringr_1.3.0          xml2_1.2.0             grid_3.5.0            
> [29] glue_1.2.0             reshape_0.8.7          data.table_1.10.4-3    R6_2.2.2              
> [33] XML_3.98-1.10          purrr_0.2.4            tidyr_0.8.0            reshape2_1.4.3        
> [37] magrittr_1.5           codetools_0.2-15       assertthat_0.2.0       bold_0.5.0            
> [41] taxize_0.9.3           stringi_1.1.7          lazyeval_0.2.1         RCurl_1.95-4.10       
> [45] zoo_1.8-1 


> On Apr 11, 2018, at 10:25 AM, Elizabeth Purdom <epurdom at stat.Berkeley.EDU> wrote:
> 
> 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 <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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