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BioC 3.5: BUILD report for cummeRbund on malbec2

This page was generated on 2017-08-16 13:14:11 -0400 (Wed, 16 Aug 2017).

Package 304/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.18.0
Loyal A. Goff
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cummeRbund
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: cummeRbund
Version: 2.18.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cummeRbund
StartedAt: 2017-08-15 18:58:50 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:59:28 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 38.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cummeRbund
###
##############################################################################
##############################################################################


* 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 /tmp/RtmpPYOIA6/Rinst43ff2ed6c8b8/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 /tmp/RtmpPYOIA6/Rinst43ff2ed6c8b8/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  /tmp/RtmpPYOIA6/Rinst43ff2ed6c8b8/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 /tmp/RtmpPYOIA6/Rinst43ff2ed6c8b8/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