Multiple platform build/check report for BioC 3.22 - BUILD results for cummeRbund on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4715
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4535
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4543
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD results for cummeRbund on nebbiolo2

To the developers/maintainers of the cummeRbund package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cummeRbund.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: cummeRbund
Version: 2.51.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 cummeRbund
StartedAt: 2025-09-11 17:02:52 -0400 (Thu, 11 Sep 2025)
EndedAt: 2025-09-11 17:04:45 -0400 (Thu, 11 Sep 2025)
EllapsedTime: 113.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 cummeRbund
###
##############################################################################
##############################################################################


* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* preparing ‘cummeRbund’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cummeRbund-example-workflow.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect,
    is.element, setdiff, setequal, union


Attaching package: ‘BiocGenerics’

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,
    aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq,
    get, grep, grepl, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table,
    tapply, unique, unsplit, 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:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
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/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cuffData.db
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading Run Info File /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/run.info
Writing runInfo Table
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading Read Group Info  /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/read_groups.info
Warning: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier().
Writing replicates Table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping geneData table
Recasting
Writing geneData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping isoformData table
Recasting
Writing isoformData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping TSSData table
Recasting
Writing TSSData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping CDSData table
Recasting
Writing CDSData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Indexing Tables...
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning: call dbDisconnect() when finished working with a connection
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Getting gene information:
	FPKM
Warning: Closing open result set, pending rows
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting isoforms information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting CDS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting TSS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting promoter information:
	distData
Warning: Closing open result set, pending rows
Getting splicing information:
	distData
Getting relCDS information:
	distData
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
--- finished re-building 'cummeRbund-example-workflow.Rnw'

--- re-building 'cummeRbund-manual.Rnw' using Sweave
Creating database /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cuffData.db
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading Run Info File /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/run.info
Writing runInfo Table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading Read Group Info  /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/read_groups.info
Writing replicates Table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Warning: Closing open result set, pending rows
Populating samples table...
Writing genes table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping geneData table
Recasting
Writing geneData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping isoformData table
Recasting
Writing isoformData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping TSSData table
Recasting
Writing TSSData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reshaping CDSData table
Recasting
Writing CDSData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Reading read group info in /tmp/RtmpBCH7q8/Rinst29687d79f6f339/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Indexing Tables...
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in result_fetch(res@ptr, n = n) :
  `dbGetQuery()`, `dbSendQuery()` and `dbFetch()` should only be used with `SELECT` queries. Did you mean `dbExecute()`, `dbSendStatement()` or `dbGetRowsAffected()`?
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic argument:
• na.rm = T
ℹ Did you misspell an argument name?
Scale for x is already present.
Adding another scale for x, which will replace the existing
scale.
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic argument:
• na.rm = T
ℹ Did you misspell an argument name?
Scale for x is already present.
Adding another scale for x, which will replace the existing
scale.
Warning: Removed 204 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: Removed 492 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: Removed 204 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: Removed 492 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: Removed 204 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: Removed 492 rows containing non-finite outside the scale range
(`stat_density()`).
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more
  information.
ℹ The deprecated feature was likely used in the cummeRbund
  package.
  Please report the issue to the authors.
Warning: The dot-dot notation (`..scaled..`) was deprecated in ggplot2
3.4.0.
ℹ Please use `after_stat(scaled)` instead.
ℹ The deprecated feature was likely used in the cummeRbund
  package.
  Please report the issue to the authors.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2
3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the cummeRbund
  package.
  Please report the issue to the authors.
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 54 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 40 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 40 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 40 rows containing missing values or values outside the
scale range (`geom_point()`).
Getting gene information:
	FPKM
Warning: Closing open result set, pending rows
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting isoforms information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting CDS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting TSS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting promoter information:
	distData
Warning: Closing open result set, pending rows
Getting splicing information:
	distData
Getting relCDS information:
	distData
Getting gene information:
	FPKM
Warning: Closing open result set, pending rows
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting isoforms information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting CDS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting TSS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting promoter information:
	distData
Warning: Closing open result set, pending rows
Getting splicing information:
	distData
Getting relCDS information:
	distData
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Scale for colour is already present.
Adding another scale for colour, which will replace the existing
scale.
Warning: No shared levels found between `names(values)` of the manual
scale and the data's colour values.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing
scale.
Warning: No shared levels found between `names(values)` of the manual
scale and the data's colour values.
Warning: No shared levels found between `names(values)` of the manual
scale and the data's colour values.
Using tracking_id, sample_name as id variables
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
`geom_smooth()` using formula = 'y ~ x'
Warning: Removed 4 rows containing non-finite outside the scale range
(`stat_smooth()`).
Using tracking_id, sample_name as id variables
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
`geom_smooth()` using formula = 'y ~ x'
Warning: Removed 4 rows containing non-finite outside the scale range
(`stat_smooth()`).
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_y_log10() :
  log-10 transformation introduced infinite values.
Warning in scale_x_log10() :
  log-10 transformation introduced infinite values.
`geom_smooth()` using formula = 'y ~ x'
Warning: Removed 4 rows containing non-finite outside the scale range
(`stat_smooth()`).
Warning: Removed 2 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 2 rows containing missing values or values outside the
scale range (`geom_point()`).
Warning: Removed 2 rows containing missing values or values outside the
scale range (`geom_point()`).
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
Using tracking_id, sample_name as id variables
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows

Error: processing vignette 'cummeRbund-manual.Rnw' failed with diagnostics:
 chunk 69 (label = sig_mat_1) 
Error : The `show_guide` argument of `layer()` was deprecated in
ggplot2 2.0.0 and is now defunct.
ℹ Please use the `show.legend` argument instead.

--- failed re-building 'cummeRbund-manual.Rnw'

SUMMARY: processing the following file failed:
  'cummeRbund-manual.Rnw'

Error: Vignette re-building failed.
Execution halted