I try to import  data from kallisto using tximport:

dds <- DESeqDataSetFromTximport(txi.kallisto, sample_id, ~condition)
Error in validObject(.Object) :
  invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should be or extend class "characterORNULL"
invalid class “SummarizedExperiment” object: 2: 'names(x)' must be NULL or a character vector with no attributes

I use this code:

txi.kallisto <- tximport(sample_id$files, type = "kallisto", txOut = TRUE,tx2gene = tx2gene)

head(txi.kallisto$counts)


dds <- DESeqDataSetFromTximport(txi.kallisto, sample_id, ~condition)

Last time this error was linked with a mix of out of date packages (SummarizedExperiment and S4Vectors). Can you update all packages with biocLite(), restart and try again?

DESeqDataSetFromTximport: Error in checkSlotAssignment