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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spliceR
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* checking for file ‘spliceR/DESCRIPTION’ ... OK
* preparing ‘spliceR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: 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, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 object is masked from ‘package:base’:
expand.grid
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
Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: RColorBrewer
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:cummeRbund':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Attaching package: 'spliceR'
The following object is masked from 'package:cummeRbund':
conditions
The following object is masked from 'package:BiocGenerics':
conditions
Creating database /tmp/Rtmp09YqVC/cuffData.db
Warning in rsqlite_fetch(res@ptr, n = n) :
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Warning in rsqlite_fetch(res@ptr, n = n) :
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Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Warning in rsqlite_fetch(res@ptr, n = n) :
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Reading Run Info File /tmp/Rtmp09YqVC/run.info
Writing runInfo Table
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Warning: Factors converted to character
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Reading Read Group Info /tmp/Rtmp09YqVC/read_groups.info
Warning: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier().
Writing replicates Table
Warning: Factors converted to character
Warning in rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/Rtmp09YqVC/genes.fpkm_tracking
Checking samples table...
Warning: Closing open result set, pending rows
Populating samples table...
Error: processing vignette 'spliceR.Rnw' failed with diagnostics:
chunk 1 (label = Cufflinks_workflow)
Error : Column name mismatch.
Execution halted