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BioC 3.3: CHECK report for flowStats on morelia

This page was generated on 2016-04-21 13:21:10 -0700 (Thu, 21 Apr 2016).

Package 411/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 3.29.2
Greg Finak and Mike Jiang
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats
Last Changed Rev: 113163 / Revision: 116626
Last Changed Date: 2016-02-01 16:40:34 -0800 (Mon, 01 Feb 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowStats
Version: 3.29.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowStats_3.29.2.tar.gz
StartedAt: 2016-04-21 02:32:06 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 02:37:11 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 304.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowStats.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowStats_3.29.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowStats.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.29.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘flowStats’ can be installed ... [18s/19s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowStats.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’ ‘fda’
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
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘flowWorkspace::getDimensions’
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
  ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’
  ‘flowViz:::plotType’ ‘flowWorkspace:::.isBoolGate’
  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:
  ‘backGating’ ‘curvPeaks’ ‘getPeakRegions’ ‘idFeaturesByBackgating’
  ‘landmarkMatrixWithoutFilterResult’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
  parameters(table), preselection = pre, scale = table@scale, bwFac =
  table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
  partial argument match of 'eval' to 'evaluate'
.normalizeGatingSet: no visible global function definition for
  ‘getNodes’
.normalizeGatingSet: no visible global function definition for ‘clone’
.normalizeGatingSet: no visible global function definition for
  ‘getGate’
.normalizeGatingSet: no visible global function definition for
  ‘getParent’
.normalizeGatingSet: no visible global function definition for
  ‘flowData<-’
.normalizeGatingSet: no visible global function definition for
  ‘flowData’
.normalizeGatingSet: no visible global function definition for
  ‘recompute’
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
SignifFeatureRegion: no visible global function definition for ‘pchisq’
density1d_simple: no visible binding for global variable ‘y’
dfltBWrange: no visible binding for global variable ‘IQR’
fdPar: no visible global function definition for ‘fd’
fdPar: no visible global function definition for ‘vec2Lfd’
fdPar: no visible global function definition for ‘norder.bspline’
fdPar: no visible global function definition for ‘int2Lfd’
hubers1: no visible global function definition for ‘pnorm’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
singletGate: no visible global function definition for ‘predict’
singletGate: no visible global function definition for ‘polygonGate’
symconv.ks: no visible global function definition for ‘fft’
symconv2D.ks: no visible global function definition for ‘fft’
symconv3D.ks: no visible global function definition for ‘fft’
symconv4D.ks: no visible global function definition for ‘fft’
warpSetNCDF: no visible global function definition for
  ‘clone.ncdfFlowSet’
addName,curv1Filter-character: no visible global function definition
  for ‘identifier’
addName,curv1Filter-character: no visible global function definition
  for ‘checkParameterMatch’
addName,curv1Filter-character: no visible global function definition
  for ‘addName’
addName,curv1Filter-logical: no visible global function definition for
  ‘addName’
addName,curv2Filter-character: no visible global function definition
  for ‘identifier’
addName,curv2Filter-character: no visible global function definition
  for ‘checkParameterMatch’
addName,curv2Filter-character: no visible global function definition
  for ‘addName’
addName,curv2Filter-character: no visible global function definition
  for ‘polygonGate’
addName,curv2Filter-logical: no visible global function definition for
  ‘addName’
densityplot,view-missing: no visible global function definition for
  ‘Data’
glines,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
glines,curv1Filter-flowFrame: no visible global function definition for
  ‘glines’
glines,curv1Filter-missing: no visible global function definition for
  ‘evalError’
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
glines,curv1Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘glines’
glines,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
glines,curv2Filter-flowFrame: no visible global function definition for
  ‘glines’
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
glines,curv2Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘glines’
glines,curv2Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘polygonGate’
glpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘flowViz.par.get’
glpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘multFiltPoints’
glpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘addName’
glpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘flowViz.par.get’
glpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘multFiltPoints’
glpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘addName’
glpolygon,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
glpolygon,curv1Filter-flowFrame: no visible global function definition
  for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
glpolygon,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
glpolygon,curv2Filter-flowFrame: no visible global function definition
  for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
glpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘polygonGate’
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘checkParameterMatch’
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘identifier’
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘colorRampPalette’
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘brewer.pal’
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘checkParameterMatch’
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘identifier’
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘colorRampPalette’
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘brewer.pal’
gpolygon,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
gpolygon,curv1Filter-flowFrame: no visible global function definition
  for ‘gpolygon’
gpolygon,curv1Filter-missing: no visible global function definition for
  ‘evalError’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
gpolygon,curv1Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘gpolygon’
gpolygon,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
gpolygon,curv2Filter-flowFrame: no visible global function definition
  for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘identifier’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
gpolygon,curv2Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult : <anonymous>: no visible
  global function definition for ‘polygonGate’
summarizeFilter,multipleFilterResult-curv1Filter: no visible global
  function definition for ‘callNextMethod’
summarizeFilter,multipleFilterResult-curv2Filter: no visible global
  function definition for ‘callNextMethod’
Undefined global functions or variables:
  Data IQR addName bogus brewer.pal callNextMethod checkParameterMatch
  clone clone.ncdfFlowSet cluster colorRampPalette evalError fd fft
  flowData flowData<- flowViz.par.get getGate getNodes getParent glines
  gpolygon group hasPeak identifier int2Lfd multFiltPoints
  norder.bspline params pchisq pnorm polygonGate predict recompute
  vec2Lfd whichS y
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("methods", "callNextMethod")
  importFrom("stats", "IQR", "fft", "pchisq", "pnorm", "predict")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [92s/103s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   29.225  5.773  38.722
gaussNorm  9.573  0.628  11.488
lymphGate  5.501  0.326   6.349
density1d  4.846  0.465   5.716
gpaSet     5.136  0.144   6.039
rangeGate  4.767  0.440   5.699
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/flowStats.Rcheck/00check.log’
for details.

flowStats.Rcheck/00install.out:

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowStats)

flowStats.Rcheck/flowStats-Ex.timings:

nameusersystemelapsed
autoGate3.2580.1293.867
binByRef1.1790.0951.395
calcPBChiSquare1.1910.0751.528
calcPearsonChi1.2710.0561.476
curv1Filter-class0.3550.0320.461
curv2Filter-class2.1450.1532.430
curvPeaks1.0440.1041.234
density1d4.8460.4655.716
gaussNorm 9.573 0.62811.488
gpaSet5.1360.1446.039
iProcrustes0.2800.0030.323
idFeaturesByBackgating2.1510.0172.543
landmarkMatrix1.3010.1131.582
lymphGate5.5010.3266.349
normalize0.0020.0000.002
plotBins1.4170.1001.740
proBin0.8360.0540.975
quadrantGate0.0010.0000.001
rangeGate4.7670.4405.699
singletGate0.0010.0000.001
warpSet29.225 5.77338.722