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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 cummeRbund
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* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* preparing ‘cummeRbund’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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
Creating database /private/tmp/RtmplhFg2J/Rinst2914621e0f84/cummeRbund/extdata/cuffData.db
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) :
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
Reading Run Info File /private/tmp/RtmplhFg2J/Rinst2914621e0f84/cummeRbund/extdata/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 /private/tmp/RtmplhFg2J/Rinst2914621e0f84/cummeRbund/extdata/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 /private/tmp/RtmplhFg2J/Rinst2914621e0f84/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: processing vignette 'cummeRbund-example-workflow.Rnw' failed with diagnostics:
chunk 3 (label = read)
Error : Column name mismatch.
Execution halted