CSAW: Error: could not find function "normOffsets"
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gthm ▴ 30
@gthm-8377
Last seen 5.0 years ago
spain

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                    

csaw edgeR chipseq • 1.8k views
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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.

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Aaron Lun ★ 28k
@alun
Last seen 7 hours ago
The city by the bay

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

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I just did:

source("https://bioconductor.org/biocLite.R")
biocLite("csaw")
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Are you using the latest version of Bioconductor and R? What is the output of sessionInfo()?

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it works after i upgrade everything to latest versions.

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