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CHECK report for flowStats on malbec2

This page was generated on 2018-10-17 08:22:43 -0400 (Wed, 17 Oct 2018).

Package 518/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 3.38.0
Greg Finak and Mike Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowStats
Branch: RELEASE_3_7
Last Commit: 06f816c
Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowStats
Version: 3.38.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowStats_3.38.0.tar.gz
StartedAt: 2018-10-16 00:27:30 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:29:37 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 127.2 seconds
RetCode: 0
Status:  OK 
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowStats_3.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowStats.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘3.38.0’
* 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 ... 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’ ‘fda’ ‘ncdfFlow’
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
Packages in Depends field not imported from:
  ‘cluster’ ‘ncdfFlow’
  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'
.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 ‘norder.bspline’
gate_singlet: no visible global function definition for ‘predict’
hubers1: no visible global function definition for ‘pnorm’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
pcout: no visible global function definition for ‘qchisq’
singletGate: no visible global function definition for ‘predict’
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’
warpSetNCDFLowMem: no visible global function definition for
  ‘clone.ncdfFlowSet’
addName,curv1Filter-character: no visible global function definition
  for ‘checkParameterMatch’
addName,curv2Filter-character: no visible global function definition
  for ‘checkParameterMatch’
glines,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
glines,curv1Filter-missing: no visible global function definition for
  ‘evalError’
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
glines,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
glpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘multFiltPoints’
glpoints,curv2Filter-flowFrame-character: no visible global function
  definition for ‘multFiltPoints’
glpolygon,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
glpolygon,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for ‘checkParameterMatch’
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 ‘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-missing: no visible global function definition for
  ‘evalError’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
gpolygon,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘colorRampPalette’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for ‘brewer.pal’
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:
  IQR bogus brewer.pal callNextMethod checkParameterMatch
  clone.ncdfFlowSet cluster colorRampPalette evalError fft group
  hasPeak multFiltPoints norder.bspline params pchisq pnorm predict
  qchisq whichS y
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("methods", "callNextMethod")
  importFrom("stats", "IQR", "fft", "pchisq", "pnorm", "predict",
             "qchisq")
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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   13.480   0.02  13.513
gaussNorm  5.384   0.04   5.431
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/flowStats.Rcheck/00check.log’
for details.



Installation output

flowStats.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowStats
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘flowStats’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowStats)

Tests output


Example timings

flowStats.Rcheck/flowStats-Ex.timings

nameusersystemelapsed
autoGate1.8440.0201.878
binByRef0.8880.0120.899
calcPBChiSquare0.6280.0280.657
calcPearsonChi0.7200.0040.724
curv1Filter-class0.2240.0000.221
curv2Filter-class1.3080.0201.330
curvPeaks0.5400.0080.549
density1d2.5440.0162.564
gaussNorm5.3840.0405.431
gpaSet2.5720.0082.593
iProcrustes0.1560.0000.153
idFeaturesByBackgating0.9760.0040.979
landmarkMatrix0.6480.0240.671
lymphGate2.8360.0522.890
normalize0.0040.0000.002
plotBins0.8320.0360.870
proBin0.5480.0280.576
quadrantGate0.0000.0000.001
rangeGate2.4520.0202.472
singletGate0.0000.0000.001
warpSet13.480 0.02013.513