Hello, I am having an error with running the command newCountDataSet() using DESeq2. Not sure if this also has to do with R 4.0? Thanks. Cheers

library(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 objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted,
lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

anyMissing, rowMedians

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

aperm, apply, rowsum

BiocManager::version() [1] ‘3.11’ package.version("DESeq2") [1] "1.28.0"

host <- read.csv("GenesPastOAojo.csv", header=TRUE, row.names=1) meta <- read.csv("PastreoidesYear-2metadata.csv", header=TRUE, row.names=1)

host.counts <- newCountDataSet(host, meta) Error in newCountDataSet(host, meta) : could not find function "newCountDataSet"

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] enAU.UTF-8/enAU.UTF-8/enAU.UTF-8/C/enAU.UTF-8/en_AU.UTF-8

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

other attached packages: [1] DESeq21.28.0 SummarizedExperiment1.18.1 DelayedArray0.14.0
[4] matrixStats0.56.0 Biobase2.48.0 GenomicRanges1.40.0
[7] GenomeInfoDb1.24.0 IRanges2.22.1 S4Vectors0.26.0
[10] BiocGenerics0.34.0

loaded via a namespace (and not attached): [1] genefilter1.70.0 locfit1.5-9.4 xfun0.13 splines4.0.0
[5] lattice0.20-41 colorspace1.4-1 vctrs0.2.4 blob1.2.1
[9] survival3.1-12 XML3.99-0.3 rlang0.4.6 pillar1.4.4
[13] glue1.4.0 DBI1.1.0 BiocParallel1.22.0 bit640.9-7
[17] RColorBrewer1.1-2 GenomeInfoDbData1.2.3 lifecycle0.2.0 zlibbioc1.34.0
[21] munsell0.5.0 gtable0.3.0 memoise1.1.0 knitr1.28
[25] geneplotter1.66.0 AnnotationDbi1.50.0 Rcpp1.0.4.6 xtable1.8-4
[29] scales1.1.0 BiocManager1.30.10 annotate1.66.0 XVector0.28.0
[33] bit1.1-15.2 ggplot23.3.0 digest0.6.25 grid4.0.0
[37] tools4.0.0 bitops1.0-6 magrittr1.5 RCurl1.98-1.2
[41] RSQLite2.2.0 tibble3.0.1 crayon1.3.4 pkgconfig2.0.3
[45] ellipsis0.3.0 Matrix1.2-18 rstudioapi0.11 R62.4.1
[49] compiler_4.0.0