[Bioc-devel] SummarizedExperiments not equal after serialisation

[Laurent Gatto]

I would appreciate some background about the following:

> suppressPackageStartupMessages(library("SummarizedExperiment"))
> set.seed(1L)
> m <- matrix(rnorm(16), ncol = 4, dimnames = list(letters[1:4], LETTERS[1:4]))
> rowdata <- DataFrame(X = 1:4, row.names = letters[1:4])
> se1 <- SummarizedExperiment(m, rowData = rowdata)
> se2 <- SummarizedExperiment(m, rowData = rowdata)
> all.equal(se1, se2)
[1] TRUE

But after serialising and reading se2, the two instances aren't equal any more:

> saveRDS(se2, file = "se2.rds")
> rm(se2)
> se2 <- readRDS("se2.rds")
> all.equal(se1, se2)
[1] "Attributes: < Component “assays”: Class definitions are not identical >"

Session information provided below.

Thank you in advance,

Laurent


R version 3.6.0 RC (2019-04-21 r76417)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
 [3] BiocParallel_1.18.0         matrixStats_0.54.0         
 [5] Biobase_2.44.0              GenomicRanges_1.36.0       
 [7] GenomeInfoDb_1.20.0         IRanges_2.18.0             
 [9] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] lattice_0.20-38        bitops_1.0-6           grid_3.6.0            
 [4] zlibbioc_1.30.0        XVector_0.24.0         Matrix_1.2-17         
 [7] tools_3.6.0            RCurl_1.95-4.12        compiler_3.6.0        
[10] GenomeInfoDbData_1.2.1