Question: Deseq2 library load error
0
gravatar for Ambika
21 months ago by
Ambika30
United States/Auburn/Auburn University
Ambika30 wrote:

Hi everyone,

I was trying to load Dseq2 library in my R studio but I got the following error. Could you help me to figure out the issue.

> 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, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, 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
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded
In addition: Warning messages:
1: package ‘S4Vectors’ was built under R version 3.4.1 
2: package ‘BiocGenerics’ was built under R version 3.4.1 
3: package ‘IRanges’ was built under R version 3.4.1 
4: package ‘GenomicRanges’ was built under R version 3.4.2 
5: package ‘GenomeInfoDb’ was built under R version 3.4.2

Thank you,

Ambika

rna-seq • 1.6k views
ADD COMMENTlink modified 21 months ago by h.mon26k • written 21 months ago by Ambika30
0
gravatar for h.mon
21 months ago by
h.mon26k
Brazil
h.mon26k wrote:

Install GenomeInfoDbData:

source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDbData")

In addition, you may want to recompile your BioConductor packages, see section Recompiling installed Bioconductor packages at https://www.bioconductor.org/install/.

ADD COMMENTlink written 21 months ago by h.mon26k

Thank you for your help H.mon

ADD REPLYlink written 21 months ago by Ambika30
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