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CHECK report for QUALIFIER on merida1

This page was generated on 2019-08-24 12:12:28 -0400 (Sat, 24 Aug 2019).

Package 1302/1760HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QUALIFIER 1.29.1
Mike Jiang
Snapshot Date: 2019-08-23 17:00:50 -0400 (Fri, 23 Aug 2019)
URL: https://git.bioconductor.org/packages/QUALIFIER
Branch: master
Last Commit: c7eb3e5
Last Changed Date: 2019-05-02 15:01:53 -0400 (Thu, 02 May 2019)
malbec1 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: QUALIFIER
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QUALIFIER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QUALIFIER_1.29.1.tar.gz
StartedAt: 2019-08-24 04:10:23 -0400 (Sat, 24 Aug 2019)
EndedAt: 2019-08-24 04:12:12 -0400 (Sat, 24 Aug 2019)
EllapsedTime: 108.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: QUALIFIER.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:QUALIFIER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings QUALIFIER_1.29.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.29.1’
* 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
  ‘gh_get_transformations’
.getQAStats.gh: no visible global function definition for
  ‘gs_get_pop_paths’
.getQAStats.gh: no visible global function definition for
  ‘gh_pop_get_data’
.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
  ‘gh_pop_get_gate’
.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
  ‘gh_pop_get_data’
.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
  ‘gh_pop_get_gate’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘gh_pop_get_proportion’
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
  ‘gh_pop_get_data’
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
  ‘gs_pop_get_parent’
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 ‘gh_pop_get_data’
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
  gh_get_transformations gh_pop_get_data gh_pop_get_gate
  gh_pop_get_proportion gray gs_get_pop_paths gs_pop_get_parent 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':
  ‘flowjo_to_gatingset’

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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.



Installation output

QUALIFIER.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL QUALIFIER
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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)

Tests output


Example timings

QUALIFIER.Rcheck/QUALIFIER-Ex.timings

nameusersystemelapsed
getQAStats0.0000.0000.001
initDB0.0140.0010.014
plot-methods0.0000.0000.001
qaCheck-methods000
qaPreprocess000
qaReport000
read.qaTask000
saveToDB0.0000.0000.001
save_db0.0000.0000.001