I have just upgraded my R to 3.2, bioconductor to 3.1 and then installed the latest DESeq2 package and now a DESeq analysis that used to work keeps failing with the same error. Here is what I have been doing:

> register(MulticoreParam(12))
> countData<-read.csv("counts.csv",header=T,row.names=1)
> colData<-read.csv("sample_meta_data.csv", header=T, row.names=1)
> dds<-DESeqDataSetFromMatrix(countData = countData, colData=colData, design = ~ line + treatment  )
# remove some genes with low counts
> dds <- estimateSizeFactors(dds)
> nc<-counts(dds, normalized=TRUE)
> filter<-rowSums(nc >= 15) >= 3
> ddsf<-dds[filter,]
# run DESeq2
>  ddsf<-DESeq(ddsf, parallel=T)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates: 12 workers
 
Error in do.call(rbind, bplapply(levels(idx), function(l) { :
  error in evaluating the argument 'args' in selecting a method for function 'do.call':
> Terminated

It takes quite a while for the error to appear (10 minutes or so?) after the message "gene-wise dispersion estimates" appears.

I have re-installed all previously installed CRAN packages now and also re-installed the BioConductor packages and nothing is showing any errors there.

Does anybody else experience problems with this latest release of DESeq2?

here is my sessionInfo:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] org.Mm.eg.db_3.1.2        RSQLite_1.0.0
 [3] DBI_0.3.1                 AnnotationDbi_1.30.1
 [5] Biobase_2.28.0            plyr_1.8.3
 [7] BiocParallel_1.2.20       gplots_2.17.0
 [9] DESeq2_1.8.1              RcppArmadillo_0.5.400.2.0
[11] Rcpp_0.12.0               GenomicRanges_1.20.6
[13] GenomeInfoDb_1.4.2        IRanges_2.2.7
[15] S4Vectors_0.6.5           BiocGenerics_0.14.0
[17] RColorBrewer_1.1-2        BiocInstaller_1.18.4

loaded via a namespace (and not attached):
 [1] futile.logger_1.4.1  XVector_0.8.0        bitops_1.0-6
 [4] futile.options_1.0.0 tools_3.2.2          rpart_4.1-10
 [7] digest_0.6.8         annotate_1.46.1      gtable_0.1.2
[10] lattice_0.20-33      proto_0.3-10         gridExtra_2.0.0
[13] genefilter_1.50.0    stringr_1.0.0        cluster_2.0.3
[16] caTools_1.17.1       gtools_3.5.0         locfit_1.5-9.1
[19] nnet_7.3-11          grid_3.2.2           XML_3.98-1.3
[22] survival_2.38-3      foreign_0.8-66       gdata_2.17.0
[25] latticeExtra_0.6-26  Formula_1.2-1        geneplotter_1.46.0
[28] ggplot2_1.0.1        reshape2_1.4.1       lambda.r_1.1.7
[31] magrittr_1.5         scales_0.3.0         Hmisc_3.16-0
[34] MASS_7.3-44          splines_3.2.2        xtable_1.7-4
[37] colorspace_1.2-6     KernSmooth_2.23-15   stringi_0.5-5
[40] acepack_1.3-3.3      munsell_0.4.2

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help

My BioConductor packages seem to be the right versions:

> BiocInstaller::biocValid()
[1] TRUE

Any hints welcome! Thanks!

hi Frank,

Thanks for reporting.

Could you send me the dds object, right before DESeq() and I can try to debug?

you can email to maintainer("DESeq2")