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Question: CSAW: Error: could not find function "normOffsets"
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gravatar for gthm
2.7 years ago by
gthm20
spain
gthm20 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 2.7 years ago by Aaron Lun20k • written 2.7 years ago by gthm20

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 2.7 years ago by gthm20
0
gravatar for Aaron Lun
2.7 years ago by
Aaron Lun20k
Cambridge, United Kingdom
Aaron Lun20k wrote:

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

ADD COMMENTlink written 2.7 years ago by Aaron Lun20k

I just did:

source("https://bioconductor.org/biocLite.R")
biocLite("csaw")
ADD REPLYlink written 2.7 years ago by gthm20

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

ADD REPLYlink written 2.7 years ago by Aaron Lun20k

it works after i upgrade everything to latest versions.

ADD REPLYlink written 2.7 years ago by gthm20
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