Package: QUALIFIER

Version: 1.27.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QUALIFIER.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings QUALIFIER_1.27.1.tar.gz

StartedAt: 2019-04-09 05:10:27 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:13:07 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 159.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: QUALIFIER.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QUALIFIER.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings QUALIFIER_1.27.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/QUALIFIER.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'QUALIFIER' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaCheck-methods.Rd:40: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaCheck-methods.Rd:131: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaReport.Rd:20: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaReport.Rd:63: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/QUALIFIER.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/QUALIFIER.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/QUALIFIER_1.27.1.tar.gz && rm -rf QUALIFIER.buildbin-libdir && mkdir QUALIFIER.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QUALIFIER.buildbin-libdir QUALIFIER_1.27.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL QUALIFIER_1.27.1.zip && rm QUALIFIER_1.27.1.tar.gz QUALIFIER_1.27.1.zip
###
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install for i386

* installing *source* package 'QUALIFIER' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QUALIFIER'
    finding HTML links ... done
    ITNQASTUDY                              html  
    QUALIFIER-package                       html  
    getQAStats                              html  
    finding level-2 HTML links ... done

    initDB                                  html  
    outlierFunctions                        html  
    plot-methods                            html  
    qaCheck-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaCheck-methods.Rd:40: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaCheck-methods.Rd:131: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
    qaPreprocess                            html  
    qaReport                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaReport.Rd:20: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpe0Uw8Q/R.INSTALL1f64340f161/QUALIFIER/man/qaReport.Rd:63: file link 'plot' in package 'QUALIFIER' does not exist and so has been treated as a topic
    qaTask-class                            html  
    read.qaTask                             html  
    saveToDB                                html  
    save_db                                 html  
** 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

install for x64

* installing *source* package 'QUALIFIER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QUALIFIER' as QUALIFIER_1.27.1.zip
* DONE (QUALIFIER)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'QUALIFIER' successfully unpacked and MD5 sums checked