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BioC 3.5: CHECK report for QUALIFIER on tokay2

This page was generated on 2017-10-18 14:21:43 -0400 (Wed, 18 Oct 2017).

Package 1041/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QUALIFIER 1.20.0
Mike Jiang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/QUALIFIER
Branch: RELEASE_3_5
Last Commit: f847b3b
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: QUALIFIER
Version: 1.20.0
Command: rm -rf QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && mkdir QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QUALIFIER.buildbin-libdir QUALIFIER_1.20.0.tar.gz >QUALIFIER.Rcheck\00install.out 2>&1 && cp QUALIFIER.Rcheck\00install.out QUALIFIER-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=QUALIFIER.buildbin-libdir --install="check:QUALIFIER-install.out" --force-multiarch --no-vignettes --timings QUALIFIER_1.20.0.tar.gz
StartedAt: 2017-10-18 02:16:55 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:19:27 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 151.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: QUALIFIER.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && mkdir QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QUALIFIER.buildbin-libdir QUALIFIER_1.20.0.tar.gz >QUALIFIER.Rcheck\00install.out 2>&1 && cp QUALIFIER.Rcheck\00install.out QUALIFIER-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=QUALIFIER.buildbin-libdir --install="check:QUALIFIER-install.out" --force-multiarch --no-vignettes --timings QUALIFIER_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/QUALIFIER.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.20.0'
* 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 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
* 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
** checking loading without being on the library search path ... 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 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/QUALIFIER.Rcheck/00check.log'
for details.


QUALIFIER.Rcheck/00install.out:


install for i386

* installing *source* package 'QUALIFIER' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'QUALIFIER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QUALIFIER' as QUALIFIER_1.20.0.zip
* DONE (QUALIFIER)

QUALIFIER.Rcheck/examples_i386/QUALIFIER-Ex.timings:

nameusersystemelapsed
getQAStats000
initDB0.010.000.01
plot-methods000
qaCheck-methods000
qaPreprocess000
qaReport000
read.qaTask000
saveToDB000
save_db000

QUALIFIER.Rcheck/examples_x64/QUALIFIER-Ex.timings:

nameusersystemelapsed
getQAStats000
initDB0.050.000.04
plot-methods000
qaCheck-methods000
qaPreprocess000
qaReport000
read.qaTask000
saveToDB000
save_db000