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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