I am re-running some DSS code that worked fine a few weeks ago, but now gives me an error when I run it again after an upgrade to 3.2.2. It seems to have something to do with the deprecation of the SummarizedExperiment() constructor and its need for a GRanges object as a second argument. Switching to the devel version of SummarizedExperiment/S4Vectors/BiocGenerics does not seem to help.
Would someone be able to help me with a quick-fire solution to this please?
Here is a screen dump:
> data_bsseq <- makeBSseqData(list(samp1, samp2, samp3, samp4, samp5, samp6), samples$Sample) Error in .local(assays, ...) : unused argument (rowData = <S4 object of class "GRanges">) > traceback() 5: .local(assays, ...) 4: SummarizedExperiment(assays = assays, rowData = gr) 3: SummarizedExperiment(assays = assays, rowData = gr) 2: BSseq(chr = alldat$chr, pos = alldat$pos, M = M, Cov = Cov) 1: makeBSseqData(list(samp1, samp2, samp3, samp4, samp5, samp6), c(samples$Sample))
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale:  LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8  LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages:  splines stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.18.4 DSS_2.6.0 bsseq_1.4.0 matrixStats_0.14.2 GenomicRanges_1.21.16 GenomeInfoDb_1.5.8  IRanges_2.3.14 S4Vectors_0.7.15 Biobase_2.29.1 BiocGenerics_0.15.6 loaded via a namespace (and not attached):  locfit_1.5-9.1 Rcpp_0.12.0 lattice_0.20-33 gtools_3.5.0 plyr_1.8.3  grid_3.2.2 scales_0.3.0 XVector_0.9.1 tools_3.2.2 munsell_0.4.2  colorspace_1.2-6 SummarizedExperiment_0.3.7