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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> 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....
