Hello,
I get the same error as Immanuel, and I think I have the most recent version of Bioconductor (3.1.1) and DESeq2 (1.6.2). However I get some warnings when I import DESeq2. I am running R version 3.1.1. Below you find all information on my session. Thanks alot. Eva
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> require("DESeq2")
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: IRanges
Attaching package: ‘IRanges’
The following objects are masked from ‘package:S4Vectors’:
aggregate.Rle, as.data.frame.DataFrame, as.data.frame.Rle,
as.data.frame.Vector, as.env, as.list.List, as.list.Rle,
as.list.SimpleList, .Call2, classNameForDisplay, compare,
countMatches, countQueryHits, countSubjectHits, DataFrame,
diff.Rle, duplicated.DataTable, duplicated.Rle, duplicated.Vector,
elementLengths, elementMetadata, elementMetadata<-, elementType,
endoapply, findMatches, findRun, fixedColumnNames, fold,
get_showHeadLines, get_showTailLines, isConstant, isEmpty,
isSingleInteger, isSingleNumber, isSingleNumberOrNA,
isSingleString, isSingleStringOrNA, isTRUEorFALSE, levels.Rle,
List, mcols, mcols<-, mean.Rle, median.Rle, mendoapply, metadata,
metadata<-, new2, nrun, phead, ptail, quantile.Rle, queryHits,
queryLength, recycleIntegerArg, recycleNumericArg, remapHits,
rename, revElements, rev.Rle, Rle, runLength, runLength<-, runmean,
runq, runsum, runValue, runValue<-, runwtsum, safeExplode,
selfmatch, setMethods, setValidity2, shiftApply, showAsCell,
SimpleList, sort.Rle, sort.Vector, strsplitAsListOfIntegerVectors,
subjectHits, subjectLength, summary.Rle, svn.time, unique.Rle,
unique.Vector, unstrsplit, values, values<-, width
The following objects are masked from ‘package:BiocGenerics’:
end<-, start<-, width, width<-
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rcpp
Loading required package: RcppArmadillo
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: multiple methods tables found for ‘width’
2: multiple methods tables found for ‘start<-’
3: multiple methods tables found for ‘width<-’
4: multiple methods tables found for ‘end<-’
5: multiple methods tables found for ‘unsplit’
6: replacing previous import by ‘IRanges::end<-’ when loading ‘GenomicRanges’
7: replacing previous import by ‘IRanges::start<-’ when loading ‘GenomicRanges’
8: replacing previous import by ‘IRanges::unsplit’ when loading ‘GenomicRanges’
9: replacing previous import by ‘IRanges::width’ when loading ‘GenomicRanges’
10: replacing previous import by ‘IRanges::width<-’ when loading ‘GenomicRanges’
11: replacing previous import by ‘IRanges::end<-’ when loading ‘XVector’
12: replacing previous import by ‘IRanges::start<-’ when loading ‘XVector’
13: replacing previous import by ‘IRanges::unsplit’ when loading ‘XVector’
14: replacing previous import by ‘IRanges::width’ when loading ‘XVector’
15: replacing previous import by ‘IRanges::width<-’ when loading ‘XVector’
16: multiple methods tables found for ‘width’
17: multiple methods tables found for ‘width’
18: multiple methods tables found for ‘start<-’
19: multiple methods tables found for ‘width<-’
20: multiple methods tables found for ‘end<-’
21: replacing previous import by ‘GenomicRanges::end<-’ when loading ‘DESeq2’
22: replacing previous import by ‘GenomicRanges::start<-’ when loading ‘DESeq2’
23: replacing previous import by ‘GenomicRanges::width’ when loading ‘DESeq2’
24: replacing previous import by ‘GenomicRanges::width<-’ when loading ‘DESeq2’
25: replacing previous import by ‘IRanges::unsplit’ when loading ‘DESeq2’
26: replacing previous import by ‘S4Vectors::aggregate.Rle’ when loading ‘DESeq2’
27: replacing previous import by ‘S4Vectors::as.data.frame.DataFrame’ when loading ‘DESeq2’
28: replacing previous import by ‘S4Vectors::as.data.frame.Rle’ when loading ‘DESeq2’
29: replacing previous import by ‘S4Vectors::as.data.frame.Vector’ when loading ‘DESeq2’
30: replacing previous import by ‘S4Vectors::as.env’ when loading ‘DESeq2’
31: replacing previous import by ‘S4Vectors::as.list.List’ when loading ‘DESeq2’
32: replacing previous import by ‘S4Vectors::as.list.Rle’ when loading ‘DESeq2’
33: replacing previous import by ‘S4Vectors::as.list.SimpleList’ when loading ‘DESeq2’
34: replacing previous import by ‘S4Vectors::.Call2’ when loading ‘DESeq2’
35: replacing previous import by ‘S4Vectors::.__C__Annotated’ when loading ‘DESeq2’
36: replacing previous import by ‘S4Vectors::.__C__characterORNULL’ when loading ‘DESeq2’
37: replacing previous import by ‘S4Vectors::.__C__DataFrame’ when loading ‘DESeq2’
38: replacing previous import by ‘S4Vectors::.__C__DataTable’ when loading ‘DESeq2’
39: replacing previous import by ‘S4Vectors::.__C__DataTableORNULL’ when loading ‘DESeq2’
40: replacing previous import by ‘S4Vectors::.__C__Hits’ when loading ‘DESeq2’
41: replacing previous import by ‘S4Vectors::classNameForDisplay’ when loading ‘DESeq2’
42: replacing previous import by ‘S4Vectors::.__C__List’ when loading ‘DESeq2’
43: replacing previous import by ‘S4Vectors::compare’ when loading ‘DESeq2’
44: replacing previous import by ‘S4Vectors::countMatches’ when loading ‘DESeq2’
45: replacing previous import by ‘S4Vectors::countQueryHits’ when loading ‘DESeq2’
46: replacing previous import by ‘S4Vectors::countSubjectHits’ when loading ‘DESeq2’
47: replacing previous import by ‘S4Vectors::.__C__Rle’ when loading ‘DESeq2’
48: replacing previous import by ‘S4Vectors::.__C__SimpleList’ when loading ‘DESeq2’
49: replacing previous import by ‘S4Vectors::.__C__Vector’ when loading ‘DESeq2’
50: replacing previous import by ‘S4Vectors::DataFrame’ when loading ‘DESeq2’
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DESeq2_1.6.2 RcppArmadillo_0.4.550.1.0
[3] Rcpp_0.11.3 GenomicRanges_1.16.4
[5] GenomeInfoDb_1.0.2 IRanges_1.22.10
[7] S4Vectors_0.4.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 annotate_1.44.0 AnnotationDbi_1.28.1
[4] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8
[7] Biobase_2.24.0 BiocParallel_1.0.0 brew_1.0-6
[10] checkmate_1.5.0 cluster_1.15.3 codetools_0.2-9
[13] colorspace_1.2-4 DBI_0.3.1 digest_0.6.4
[16] fail_1.2 foreach_1.4.2 foreign_0.8-61
[19] Formula_1.1-1 genefilter_1.46.1 geneplotter_1.44.0
[22] ggplot2_1.0.0 grid_3.1.1 gtable_0.1.2
[25] Hmisc_3.14-6 iterators_1.0.7 lattice_0.20-29
[28] latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-34
[31] munsell_0.4.2 nnet_7.3-8 plyr_1.8.1
[34] proto_0.3-10 RColorBrewer_1.0-5 reshape2_1.4
[37] rpart_4.1-8 RSQLite_1.0.0 scales_0.2.4
[40] sendmailR_1.2-1 splines_3.1.1 stringr_0.6.2
[43] survival_2.37-7 tools_3.1.1 XML_3.96-1.1
[46] xtable_1.7-1 XVector_0.4.0
> dds <- makeExampleDESeqDataSet(n=12)
Error in ncol(mcols(dds)) :
error in evaluating the argument 'x' in selecting a method for function 'ncol': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘mcols’ for signature ‘"DESeqDataSet"’
Can you edit your question to provide the output of
sessionInfo()
after you get this error, please?Did you upgrade your entire "bioconductor stack" to 3.0?
Yes, I'd agree with Steve.
See instructions for upgrading all packages here: "Upgrading installed Bioconductor packages"
http://www.bioconductor.org/install/#update-bioconductor-packages