Hi Bioc,

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?

Best,

Tim

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:
 [1] 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   
 [6] LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BiocInstaller_1.18.4  DSS_2.6.0             bsseq_1.4.0           matrixStats_0.14.2    GenomicRanges_1.21.16 GenomeInfoDb_1.5.8   
 [7] IRanges_2.3.14        S4Vectors_0.7.15      Biobase_2.29.1        BiocGenerics_0.15.6  

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1             Rcpp_0.12.0                lattice_0.20-33            gtools_3.5.0               plyr_1.8.3                
 [6] grid_3.2.2                 scales_0.3.0               XVector_0.9.1              tools_3.2.2                munsell_0.4.2             
[11] colorspace_1.2-6           SummarizedExperiment_0.3.7

Hi Tim,

You're using a mix of release (BioC 3.1) and devel (BioC 3.2) packages:

• from release: BiocInstaller 1.18.4, DSS 2.6.0, bsseq 1.4.0, matrixStats 0.14.2
• from devel: GenomicRanges_1.21.16, GenomeInfoDb 1.5.8, IRanges 2.3.14, S4Vectors 0.7.15, Biobase 2.29.1, BiocGenerics 0.15.6, and SummarizedExperiment (this one doesn't exist in release, it's a new package)

This is not good as it almost always breaks things. Please use biocValid() from the BiocInstaller package to fix. Always install packages with biocLite() and from our standard package repos (i.e. biocLite("pkgname") and not biocLite("github_repo/pkgname")).

Cheers,

H.

Fixed from the suggested output from biocValid(), thanks Hervé Pagès. I had the same output before even switching to devel, but there must have been a rogue devel package in there somewhere already.

Cheers,
Tim