I am running code that I have run many times over the last two months and suddenly it stopped working. I checked my older backup copies to ensure I hadn't accidentally deleted something. Everything is exactly as it has been but it now throws an error.

Import my raw count data/processing:

countData <- read.csv(file = "countData.csv", header = T)
rownames(countData) <- countData[ ,1]
countData[ ,1] <- NULL

rownames(metaTable) <- metaTable[ ,1]   # Set first column to row names
metaTable[ ,1] <- NULL

Create DESeq object (note: my metaTable is not shown in this post):

dd <- DESeqDataSetFromMatrix(countData = countData, colData = metaTable, design = ~ condition)

This produces (sample names altered):

class: DESeqDataSet
dim: 47729 42
metadata(1): version
assays(1): counts
rownames(47729): ENSMUSG00000102693 ENSMUSG00000064842 ...
  ENSMUSG00000096730 ENSMUSG00000095742
rowData names(0):
colnames(42): SAMPLE1 SAMPLE1 ... SAMPLE41 SAMPLE42
colData names(5): LibraryLayout fastq condition technical Counts

Collapse technical replicates:

dd$technical <- gsub("_T1|_T2", "", row.names(metaTable))
ddRep <- collapseReplicates(dd, groupby = dd$technical)

This produces (sample names altered):

class: DESeqDataSet
dim: 47729 21
metadata(1): version
assays(1): counts
rownames(47729): ENSMUSG00000102693 ENSMUSG00000064842 ...
  ENSMUSG00000096730 ENSMUSG00000095742
rowData names(0):
colnames(21): SAMPLE1 SAMPLE2 ... SAMPLE20 SAMPLE21
colData names(6): LibraryLayout fastq ... Counts sizeFactor

Normalize:

ddRep <- estimateSizeFactors(ddRep)
normCounts <- as.data.frame(counts(ddRep, normalize = T))

Then I get this error:

Error in (function (classes, fdef, mtable)
   unable to find an inherited method for function 'counts' for signature '"DESeqDataSet"'

Session info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8      
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C             
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] BiocInstaller_1.22.3       RDAVIDWebService_1.10.0    GOstats_2.38.1           
 [4] Category_2.38.0            Matrix_1.2-7.1             graph_1.50.0             
 [7] RColorBrewer_1.1-2         pheatmap_1.0.8             reshape2_1.4.1           
[10] ggplot2_2.1.0              org.Mm.eg.db_3.3.0         AnnotationDbi_1.34.4     
[13] DESeq2_1.12.4              SummarizedExperiment_1.2.3 Biobase_2.32.0           
[16] GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1            
[19] S4Vectors_0.10.3           BiocGenerics_0.18.0      

loaded via a namespace (and not attached):
 [1] genefilter_1.54.2      locfit_1.5-9.1         splines_3.3.1        
 [4] rJava_0.9-8            lattice_0.20-34        colorspace_1.2-6     
 [7] chron_2.3-47           survival_2.39-5        RBGL_1.48.1          
[10] XML_3.98-1.4           foreign_0.8-67         DBI_0.5-1            
[13] BiocParallel_1.6.6     plyr_1.8.4             stringr_1.1.0        
[16] zlibbioc_1.18.0        munsell_0.4.3          gtable_0.2.0         
[19] latticeExtra_0.6-28    geneplotter_1.50.0     GSEABase_1.34.1      
[22] Rcpp_0.12.7            acepack_1.3-3.3        xtable_1.8-2         
[25] scales_0.4.0           Hmisc_3.17-4           annotate_1.50.1      
[28] XVector_0.12.1         gridExtra_2.2.1        stringi_1.1.2        
[31] grid_3.3.1             tools_3.3.1            bitops_1.0-6         
[34] magrittr_1.5           RCurl_1.95-4.8         RSQLite_1.0.0        
[37] Formula_1.2-1          cluster_2.0.5          GO.db_3.3.0          
[40] data.table_1.9.6       AnnotationForge_1.14.2 rpart_4.1-10         
[43] nnet_7.3-12          

What about this:

library(DESeq2)
dds <- makeExampleDESeqDataSet()
head(​counts(dds))