hi Andrea, I sent out an email to bioc-devel at the same time as you :)
https://stat.ethz.ch/pipermail/bioc-devel/2015-April/007269.html I think this might be fixed already, but I didn't have time to try out GenomicRanges 1.19.51 yet. I will try soon, and if this doesn't fix it, I have a hack to ensure dimnames are consistent for every set. So either way everything should be resolved today. best Mike On Fri, Apr 3, 2015 at 7:37 AM, Andrea Rau <andrea....@jouy.inra.fr> wrote: > Hello, > > I am the maintainer of a Bioconductor package called 'HTSFilter' that > imports DESeq2. On today's build report, I see that my package (as well as > DESeq2 and all of the other packages that import it) is showing an error > message which seems to arise from a recent change in the DESeq2 code dealing > with the dimnames of a DESeqDataSet object. The error message in my package > reads: > > Error in `assays<-`(`*tmp*`, value = <S4 object of class > structure("SimpleList", package = "S4Vectors")>) : > 'dimnames' differ between assay elements > > and seems to occur when calling the DESeq function (right after the > "gene-wise dispersion estimates" message is printed). I know that today is > the deadline for fixing errors prior to release, so the time-frame is > somewhat short to fix errors. To ensure that my package isn't withheld from > release, should I retrograde to the last stable version of DESeq2 rather > than using dev? > > Thanks for your help, > Andrea > > Here is some code + sessionInfo that illustrate the error: > >> library(HTSFilter) >> library(DESeq2) >> library(Biobase) >> data(sultan) >> conds <- pData(sultan)$cell.line >> dds <- DESeqDataSetFromMatrix(countData = exprs(sultan), > + colData = data.frame(cell.line = conds), > + design = ~ cell.line) >> dds <- DESeq(dds) > estimating size factors > estimating dispersions > gene-wise dispersion estimates > Error in `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">) : > 'dimnames' differ between assay elements >> sessionInfo() > R version 3.2.0 beta (2015-04-01 r68134) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 7 x64 (build 7601) Service Pack 1 > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > LC_MONETARY=French_France.1252 > [4] LC_NUMERIC=C LC_TIME=French_France.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] DESeq2_1.7.46 RcppArmadillo_0.4.650.1.1 Rcpp_0.11.5 > GenomicRanges_1.19.50 > [5] GenomeInfoDb_1.3.16 IRanges_2.1.43 S4Vectors_0.5.22 > HTSFilter_1.7.0 > [9] Biobase_2.27.3 BiocGenerics_0.13.10 > > loaded via a namespace (and not attached): > [1] RColorBrewer_1.1-2 futile.logger_1.4 plyr_1.8.1 > XVector_0.7.4 tools_3.2.0 > [6] futile.options_1.0.0 rpart_4.1-9 digest_0.6.8 > annotate_1.45.4 RSQLite_1.0.0 > [11] gtable_0.1.2 lattice_0.20-31 DBI_0.3.1 > proto_0.3-10 DESeq_1.19.0 > [16] cluster_2.0.1 genefilter_1.49.2 stringr_0.6.2 > locfit_1.5-9.1 nnet_7.3-9 > [21] grid_3.2.0 AnnotationDbi_1.29.20 XML_3.98-1.1 > survival_2.38-1 BiocParallel_1.1.21 > [26] foreign_0.8-61 latticeExtra_0.6-26 Formula_1.2-0 > limma_3.23.11 geneplotter_1.45.0 > [31] ggplot2_1.0.1 reshape2_1.4.1 lambda.r_1.1.7 > edgeR_3.9.14 Hmisc_3.15-0 > [36] MASS_7.3-40 scales_0.2.4 splines_3.2.0 > colorspace_1.2-6 xtable_1.7-4 > [41] acepack_1.3-3.3 munsell_0.4.2 > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel