[Bioc-devel] Build error for DESeq2 dev causing error in other package builds

[Andrea Rau]

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




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