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

Fri, Apr 3, 2015 5:32 AM

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

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

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