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Question: CSAW: Error: could not find function "normOffsets"
0
gravatar for gthm
24 months ago by
gthm0
spain
gthm0 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 24 months ago by Aaron Lun17k • written 24 months ago by gthm0

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 24 months ago by gthm0
0
gravatar for Aaron Lun
24 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

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

ADD COMMENTlink written 24 months ago by Aaron Lun17k

I just did:

source("https://bioconductor.org/biocLite.R")
biocLite("csaw")
ADD REPLYlink written 24 months ago by gthm0

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

ADD REPLYlink written 24 months ago by Aaron Lun17k

it works after i upgrade everything to latest versions.

ADD REPLYlink written 24 months ago by gthm0
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