DESeq2 error in DESeqDataSetFromMatrix and SummarizedExperiment !

Question

[super]

Hi All

I have a simple question. When I ran DESeq2, I got the error.

sampleclass<- data.frame(condition=factor(c(rep("C1",3),rep("C2",3))))
dds<-DESeqDataSetFromMatrix(countData=counts, colData= sampleclass, design=~condition)

Error in SummarizedExperiment(assays = SimpleList(counts = countData), 
  The SummarizedExperiment class defined in the GenomicRanges package is
  deprecated and being replaced with the RangedSummarizedExperiment class
  defined in the new SummarizedExperiment package. Please make sure to
  install the SummarizedExperiment package before you attempt to call the
  SummarizedExperiment() constructor function. Note that this will return
  a RangedSummarizedExperiment instance instead of a SummarizedExperiment
  instance.

> head(counts)
                   C1.R1 C1.R2 C1.R3 C2.R1 C2.R2 C2.R3
ENSRNOG00000000001   516   498   451   328   389   424
ENSRNOG00000000007     5     4     4     6     1     1
ENSRNOG00000000008     9     2     7     3     4     4
ENSRNOG00000000009     1     2     6     0     1     2
ENSRNOG00000000010     1     0     3     0     0     0
ENSRNOG00000000012     1     0     2     0     0     0
> head(sampleclass)
  condition
1        C1
2        C1
3        C1
4        C2
5        C2
6        C2

Why? I have installed the latest version of SummarizedExperiment().

[Devon Ryan]

Make sure you have the most recent version of everything. It's likely that this was addressed in the most recent version of DESeq2.