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

[Michael Love]

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.rau at 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
>
>
>