Search
Question: CSAW: Error: could not find function "normOffsets"
0
gravatar for gthm
2.2 years ago by
gthm10
spain
gthm10 wrote:

I am trying to run csaw but I am getting the following error:

Error: could not find function "normOffsets".

I could not see it either in the functions available.

> library(csaw)
Loading required package: GenomicRanges
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 object is masked from ‘package:stats’:

    xtabs

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

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

Loading required package: S4Vectors
Loading required package: stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: GenomeInfoDb
> ?norm
?norm                                               ?normalizePath
?normalize                                          ?normalizeSingleBracketReplacementValue
?normalize,SummarizedExperiment-method              ?normalizeSingleBracketReplacementValue,ANY-method
?normalizeCounts                                    ?normalizeSingleBracketSubscript
?normalizeDoubleBracketSubscript                    

ADD COMMENTlink modified 2.2 years ago by Aaron Lun18k • written 2.2 years ago by gthm10

One thing I did is to copy paste the entire function from github https://github.com/Bioconductor-mirror/csaw/blob/master/R/normOffsets.R 

and it seems to be working.

ADD REPLYlink written 2.2 years ago by gthm10
0
gravatar for Aaron Lun
2.2 years ago by
Aaron Lun18k
Cambridge, United Kingdom
Aaron Lun18k wrote:

Are you using the latest version of csaw? Older versions will not have the normOffsets function.

ADD COMMENTlink written 2.2 years ago by Aaron Lun18k

I just did:

source("https://bioconductor.org/biocLite.R")
biocLite("csaw")
ADD REPLYlink written 2.2 years ago by gthm10

Are you using the latest version of Bioconductor and R? What is the output of sessionInfo()?

ADD REPLYlink written 2.2 years ago by Aaron Lun18k

it works after i upgrade everything to latest versions.

ADD REPLYlink written 2.2 years ago by gthm10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 182 users visited in the last hour