QUALIFIER 1.20.0
Mike Jiang
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/QUALIFIER | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings QUALIFIER_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.20.0’
* 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 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 loading without being on the library search path ... 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:
‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
‘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 ... OK
* 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’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘QUALIFIER-plot-MNC-scatter.png’, ‘QUALIFIER-plot-subset2.png’,
‘QUALIFIER.Rmd’
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.