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BioC 3.4: CHECK report for flowStats on zin1

This page was generated on 2016-09-21 03:36:46 -0700 (Wed, 21 Sep 2016).

Package 431/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 3.31.4
Greg Finak and Mike Jiang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats
Last Changed Rev: 120699 / Revision: 121152
Last Changed Date: 2016-09-02 13:04:39 -0700 (Fri, 02 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (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: 3.31.4
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings flowStats_3.31.4.tar.gz
StartedAt: 2016-09-20 06:32:04 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:34:34 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 150.6 seconds
RetCode: 0
Status:  OK 
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings flowStats_3.31.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/flowStats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.31.4’
* 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 ‘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’
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 fd fft group
  hasPeak int2Lfd multFiltPoints norder.bspline params pchisq pnorm
  predict qchisq vec2Lfd 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   18.076  0.036  18.109
gaussNorm  6.164  0.036   6.204
* 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-3.4-bioc/meat/flowStats.Rcheck/00check.log’
for details.


flowStats.Rcheck/00install.out:

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowStats)

flowStats.Rcheck/flowStats-Ex.timings:

nameusersystemelapsed
autoGate2.3760.0962.490
binByRef0.8320.0480.880
calcPBChiSquare0.8520.0640.914
calcPearsonChi0.9040.0560.961
curv1Filter-class0.1960.0000.207
curv2Filter-class1.3640.0201.385
curvPeaks0.7520.0640.815
density1d3.2680.1083.400
gaussNorm6.1640.0366.204
gpaSet3.4400.0363.483
iProcrustes0.160.000.16
idFeaturesByBackgating1.2040.0161.218
landmarkMatrix0.9160.1321.046
lymphGate3.9120.0683.980
normalize0.0040.0000.001
plotBins1.0240.2601.285
proBin0.5880.2320.819
quadrantGate000
rangeGate2.9880.2683.257
singletGate000
warpSet18.076 0.03618.109