Package: QUALIFIER

Version: 1.27.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QUALIFIER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QUALIFIER_1.27.1.tar.gz

StartedAt: 2019-04-09 02:56:18 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:58:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 110.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: QUALIFIER.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QUALIFIER.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QUALIFIER_1.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/QUALIFIER.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QUALIFIER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QUALIFIER’ version ‘1.27.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'flowCore', 'flowViz', 'ncdfFlow', 'flowWorkspace', 'data.table',
  'reshape'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QUALIFIER’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘flowViz’ ‘flowWorkspace’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘flowViz’ ‘grDevices’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘data.table’ ‘flowCore’ ‘flowViz’ ‘ncdfFlow’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘flowWorkspace:::mkformula’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘flowWorkspace:::.formulaParser’ ‘flowWorkspace:::.getPopStat’
  ‘lattice:::calculateGridLayout’ ‘lattice:::checkArgsAndCall’
  ‘lattice:::chooseFace’ ‘lattice:::compute.layout’
  ‘lattice:::drawInViewport’ ‘lattice:::evaluate.legend’
  ‘lattice:::getFunctionOrName’ ‘lattice:::getLabelList’
  ‘lattice:::grobFromLabelList’ ‘lattice:::lattice.getStatus’
  ‘lattice:::lattice.setStatus’ ‘lattice:::layoutNCol’
  ‘lattice:::layoutNRow’ ‘lattice:::paste.and.draw’
  ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getName’ ‘height’ ‘width’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.TubeNameMapping: no visible global function definition for ‘pData’
.addStats: no visible global function definition for ‘getData’
.addStats: no visible binding for global variable ‘value’
.addStats: no visible global function definition for ‘:=’
.addStats: no visible binding for global variable ‘stats’
.addStats: no visible binding for global variable ‘sid’
.addStats: no visible binding for global variable ‘channel’
.addStats: no visible binding for global variable ‘stain’
.addStats: no visible binding for global variable ‘population’
.addStats: no visible binding for global variable ‘node’
.addStats: no visible global function definition for ‘setcolorder’
.addStats: no visible global function definition for ‘rbindlist’
.getQAStats.env: no visible global function definition for ‘:=’
.getQAStats.env: no visible global function definition for ‘rbindlist’
.getQAStats.env: no visible binding for global variable ‘sid’
.getQAStats.gh: no visible global function definition for ‘sampleNames’
.getQAStats.gh: no visible global function definition for
  ‘getTransformations’
.getQAStats.gh: no visible global function definition for ‘getNodes’
.getQAStats.gh: no visible global function definition for ‘getData’
.getQAStats.gh: no visible global function definition for ‘pData’
.getQAStats.gh: no visible global function definition for ‘parameters’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘getGate’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘parameters’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘data.table’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘exprs’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘rbindlist’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘getData’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘:=’
.getQAStats.gh : <anonymous>: no visible binding for global variable
  ‘node’
.getQAStats.gh : <anonymous>: no visible binding for global variable
  ‘population’
.getQAStats.gh: no visible global function definition for ‘rbindlist’
.parseTubeID: no visible global function definition for ‘pData’
.parseTubeID: no visible global function definition for ‘pData<-’
.qaCheck: no visible global function definition for ‘getData’
.qaCheck: no visible global function definition for ‘rename’
.qaCheck : .funcOutlierGrp: no visible global function definition for
  ‘IQR’
.qaCheck : .funcOutlierGrp: no visible binding for global variable
  ‘.SD’
.qaCheck : .funcOutlierGrp: no visible binding for global variable ‘V1’
.qaCheck : .funcOutlierGrp: no visible binding for global variable
  ‘sid’
.qaCheck: no visible binding for global variable ‘.SD’
.qaCheck: no visible binding for global variable ‘V1’
.qaCheck : .funcOutlier: no visible global function definition for
  ‘as.formula’
.qaCheck : .funcOutlier: no visible binding for global variable ‘sid’
.queryStats : <anonymous>: no visible global function definition for
  ‘pData’
.queryStats: no visible global function definition for ‘pData’
.queryStats: no visible binding for global variable ‘stats’
.read.qaTask : <anonymous>: no visible binding for global variable
  ‘aoutlierFunc_args’
.read.qaTask : <anonymous>: no visible global function definition for
  ‘new’
.read.qaTask : <anonymous>: no visible global function definition for
  ‘as.formula’
.setupPlotTheme: no visible global function definition for
  ‘standard.theme’
.setupPlotTheme: no visible global function definition for ‘gray’
.timelineplot: no visible global function definition for ‘exprs’
.timelineplot: no visible global function definition for ‘median’
clearCheck: no visible global function definition for ‘getData’
createDbSchema: no visible global function definition for ‘rename’
load_db: no visible global function definition for ‘l_ply’
load_db : <anonymous>: no visible global function definition for
  ‘load_gs’
makeQaTask: no visible global function definition for ‘new’
makeQaTask: no visible global function definition for ‘as.formula’
outlier.norm: no visible global function definition for ‘median’
outlier.norm: no visible global function definition for ‘mad’
outlier.norm: no visible global function definition for ‘pnorm’
outlier.plot: no visible global function definition for ‘abline’
outlier.t: no visible global function definition for ‘optim’
outlier.t : <anonymous>: no visible global function definition for ‘dt’
outlier.t: no visible global function definition for ‘pt’
panel.bwplotEx: no visible global function definition for
  ‘trellis.par.get’
panel.bwplotEx: no visible global function definition for
  ‘current.panel.limits’
panel.bwplotEx: no visible global function definition for ‘:=’
panel.bwplotEx: no visible binding for global variable ‘.BY’
panel.bwplotEx: no visible binding for global variable ‘.SD’
panel.bwplotEx: no visible global function definition for
  ‘panel.polygon’
panel.bwplotEx: no visible global function definition for
  ‘panel.segments’
panel.bwplotEx: no visible global function definition for
  ‘panel.points’
panel.bwplotEx: no visible binding for global variable ‘outlier’
panel.bwplotEx: no visible binding for global variable ‘gOutlier’
panel.xyplot.flowsetEx: no visible global function definition for
  ‘panel.xyplot.flowset’
panel.xyplot.qa: no visible global function definition for ‘coef’
panel.xyplot.qa: no visible global function definition for ‘pt’
panel.xyplot.qa: no visible global function definition for
  ‘coefficients’
panel.xyplot.qa: no visible global function definition for ‘panel.text’
panel.xyplot.qa: no visible global function definition for ‘quantile’
panel.xyplot.qa: no visible global function definition for
  ‘panel.abline’
panel.xyplotEx: no visible global function definition for
  ‘trellis.par.get’
panel.xyplotEx: no visible binding for global variable ‘panel.grid’
panel.xyplotEx: no visible binding for global variable ‘panel.abline’
panel.xyplotEx: no visible global function definition for
  ‘panel.superpose’
panel.xyplotEx: no visible global function definition for
  ‘panel.points’
panel.xyplotEx: no visible global function definition for ‘panel.lines’
panel.xyplotEx: no visible global function definition for
  ‘panel.lmline’
panel.xyplotEx: no visible global function definition for ‘panel.loess’
panel.xyplotEx: no visible global function definition for
  ‘panel.linejoin’
plot.qaTask: no visible global function definition for ‘description’
plot.qaTask: no visible global function definition for
  ‘lattice.options’
plot.qaTask: no visible global function definition for ‘getData’
plot.qaTask: no visible global function definition for ‘:=’
plot.qaTask: no visible binding for global variable ‘outlier’
plot.qaTask: no visible binding for global variable ‘gOutlier’
plot.qaTask: no visible global function definition for ‘rename’
plot.qaTask: no visible global function definition for ‘dev.off’
plot.qaTask: no visible global function definition for ‘png’
plot.trellisEx: no visible binding for global variable
  ‘packet.panel.default’
plot.trellisEx: no visible global function definition for
  ‘lattice.getOption’
plot.trellisEx: no visible global function definition for ‘dev.list’
plot.trellisEx: no visible global function definition for
  ‘trellis.device’
plot.trellisEx: no visible global function definition for
  ‘trellis.par.get’
plot.trellisEx: no visible global function definition for
  ‘trellis.par.set’
plot.trellisEx: no visible global function definition for
  ‘lattice.options’
plot.trellisEx: no visible global function definition for
  ‘trellis.grobname’
plot.trellisEx: no visible global function definition for
  ‘trellis.vpname’
plot.trellisEx: no visible global function definition for ‘par’
plot.trellisEx: no visible global function definition for ‘panel.fill’
proportion.outliers.mle: no visible global function definition for
  ‘optim’
proportion.outliers.mle : <anonymous>: no visible global function
  definition for ‘dbeta’
proportion.outliers.mle: no visible global function definition for
  ‘pbeta’
proportion.outliers.robust: no visible global function definition for
  ‘optim’
proportion.outliers.robust : <anonymous>: no visible global function
  definition for ‘median’
proportion.outliers.robust : <anonymous>: no visible global function
  definition for ‘mad’
proportion.outliers.robust: no visible global function definition for
  ‘pbeta’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getGate’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getProp’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘pData’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘parameters’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getData’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘extends’
qa.GroupPlot : <anonymous>: no visible binding for global variable
  ‘channel’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getParent’
qa.GroupPlot: no visible global function definition for ‘flowSet’
qa.GroupPlot: no visible global function definition for ‘as.formula’
qa.GroupPlot: no visible binding for global variable ‘name’
qaWrite.list: no visible global function definition for ‘getData’
qaWrite.summary: no visible global function definition for ‘getData’
qaWrite.summary: no visible global function definition for ‘pData’
qaWrite.summary: no visible global function definition for ‘cast’
qaWrite.task: no visible global function definition for ‘getData’
qaWrite.task: no visible global function definition for ‘pData’
qaWrite.task: no visible global function definition for ‘rename’
qaWrite.task: no visible global function definition for ‘description’
qaWrite.task: no visible global function definition for ‘as.formula’
qaWrite.task: no visible global function definition for ‘melt’
qaWrite.task: no visible global function definition for ‘cast’
qaWrite.task : <anonymous>: no visible global function definition for
  ‘getData’
read.qaTask: no visible global function definition for ‘read.csv’
read.qaTask: no visible global function definition for ‘fread’
saveToDB: no visible global function definition for ‘pData’
saveToDB: no visible global function definition for ‘fread’
saveToDB: no visible binding for global variable ‘name’
saveToDB: no visible global function definition for ‘sampleNames’
saveToDB: no visible global function definition for ‘pData<-’
saveToDB: no visible global function definition for ‘getData’
save_db: no visible global function definition for ‘l_ply’
save_db : <anonymous>: no visible global function definition for
  ‘save_gs’
stripEx: no visible global function definition for ‘trellis.par.get’
stripEx: no visible global function definition for ‘trellis.grobname’
getQAStats,GatingSet: no visible global function definition for ‘pData’
getQAStats,GatingSet: no visible global function definition for
  ‘sampleNames’
queryStats,qaTask: no visible global function definition for ‘getData’
show,qaTask: no visible global function definition for ‘description’
Undefined global functions or variables:
  .BY .SD := IQR V1 abline aoutlierFunc_args as.formula cast channel
  coef coefficients current.panel.limits data.table dbeta description
  dev.list dev.off dt exprs extends flowSet fread gOutlier getData
  getGate getNodes getParent getProp getTransformations gray l_ply
  lattice.getOption lattice.options load_gs mad median melt name new
  node optim outlier pData pData<- packet.panel.default panel.abline
  panel.fill panel.grid panel.linejoin panel.lines panel.lmline
  panel.loess panel.points panel.polygon panel.segments panel.superpose
  panel.text panel.xyplot.flowset par parameters pbeta png pnorm
  population pt quantile rbindlist read.csv rename sampleNames save_gs
  setcolorder sid stain standard.theme stats trellis.device
  trellis.grobname trellis.par.get trellis.par.set trellis.vpname value
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "gray", "png")
  importFrom("graphics", "abline", "par")
  importFrom("methods", "extends", "new")
  importFrom("stats", "IQR", "as.formula", "coef", "coefficients",
             "dbeta", "dt", "mad", "median", "optim", "pbeta", "pnorm",
             "pt", "quantile")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getQAStats.Rd':
  ‘parseWorkspace’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘QUALIFIER-plot-MNC-scatter.png’, ‘QUALIFIER-plot-subset2.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL QUALIFIER
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘QUALIFIER’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘QUALIFIER.Rmd’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (QUALIFIER)

name	user	system	elapsed
getQAStats	0	0	0
initDB	0.003	0.000	0.002
plot-methods	0.000	0.000	0.001
qaCheck-methods	0	0	0
qaPreprocess	0.001	0.000	0.000
qaReport	0.000	0.000	0.001
read.qaTask	0	0	0
saveToDB	0.000	0.000	0.001
save_db	0	0	0