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Question: CummeRbund fail with example directory
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gravatar for tommy.vo
11 months ago by
tommy.vo0
tommy.vo0 wrote:

Hello, I tried to run readcufflinks() in R version 3.3.3 on Mac using the package's example directory but it failed. I show my simple input R commands and the outputs: 

R version 3.3.3 (2017-03-06) -- "Another Canoe"
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Platform: x86_64-apple-darwin13.4.0 (64-bit)

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> library(cummeRbund)
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, xtabs

The following objects are masked from ‘package:base’:
  
  anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:
  
  hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:
  
  colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':
  
  promoters

The following object is masked from 'package:IRanges':
  
  promoters

The following object is masked from 'package:BiocGenerics':
  
  conditions

> readCufflinks(dir=system.file("extdata", package="cummeRbund"))
CuffSet instance with:
0 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS

 

Does anyone know a solution to this? Or, if this is enough info to know what's going wrong? I don't think the output from the example workflow should be 0 of everything....

 

 

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