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BioC 3.5: CHECK report for flowQ on toluca2

This page was generated on 2017-04-19 13:57:55 -0400 (Wed, 19 Apr 2017).

Package 464/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowQ 1.35.1
Mike Jiang
Snapshot Date: 2017-04-18 17:17:18 -0400 (Tue, 18 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ
Last Changed Rev: 127583 / Revision: 128863
Last Changed Date: 2017-03-21 13:32:42 -0400 (Tue, 21 Mar 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 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: flowQ
Version: 1.35.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.35.1.tar.gz
StartedAt: 2017-04-19 03:33:18 -0400 (Wed, 19 Apr 2017)
EndedAt: 2017-04-19 03:38:03 -0400 (Wed, 19 Apr 2017)
EllapsedTime: 284.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowQ.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowQ.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQ’ version ‘1.35.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘outliers’ ‘lattice’ ‘flowViz’ ‘mvoutlier’ ‘bioDist’
  ‘parody’ ‘RColorBrewer’ ‘latticeExtra’
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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowQ’ 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:
  ‘methods’ ‘BiocGenerics’ ‘flowViz’
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
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘bioDist’ ‘flowViz’ ‘lattice’ ‘latticeExtra’
  ‘mvoutlier’ ‘outliers’ ‘parody’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mySd: no visible binding for global variable ‘sd’
.mySd: no visible global function definition for ‘sd’
.mybw.nrd0: no visible global function definition for ‘IQR’
evaluateProcess: multiple local function definitions for ‘efun’ with
  different formal arguments
failedProcesses: no visible global function definition for ‘listLen’
normalizeSets : <anonymous>: no visible global function definition for
  ‘warpSet’
outlierD : <anonymous>: no visible global function definition for
  ‘dixon.test’
outlierG : <anonymous>: no visible global function definition for
  ‘grubbs.test’
outlierX2 : <anonymous>: no visible global function definition for
  ‘chisq.out.test’
outlierX2 : <anonymous>: no visible global function definition for
  ‘var’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘colorRampPalette’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘brewer.pal’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘pcout’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘xyplot’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘extendrange’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘simpleKey’
qaProcess.2DStatsPlot: no visible global function definition for
  ‘dev.off’
qaProcess.BoundaryPlot: no visible global function definition for
  ‘colorRampPalette’
qaProcess.BoundaryPlot: no visible global function definition for
  ‘brewer.pal’
qaProcess.BoundaryPlot: no visible global function definition for
  ‘barchart’
qaProcess.BoundaryPlot: no visible global function definition for
  ‘simpleKey’
qaProcess.BoundaryPlot: no visible global function definition for
  ‘dev.off’
qaProcess.DensityPlot: no visible global function definition for
  ‘colorRampPalette’
qaProcess.DensityPlot: no visible global function definition for
  ‘brewer.pal’
qaProcess.DensityPlot: no visible global function definition for
  ‘density’
qaProcess.DensityPlot: no visible global function definition for
  ‘KLdist.matrix’
qaProcess.DensityPlot: no visible global function definition for
  ‘xyplot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible global function definition for
  ‘simpleKey’
qaProcess.DensityPlot: no visible global function definition for
  ‘densityplot’
qaProcess.DensityPlot : <anonymous>: no visible binding for global
  variable ‘panel.xyplot’
qaProcess.DensityPlot : <anonymous>: no visible global function
  definition for ‘trellis.panelArgs’
qaProcess.DensityPlot: no visible global function definition for
  ‘dev.off’
qaProcess.DensityPlot: no visible global function definition for
  ‘calout.detect’
qaProcess.ECDFPlot: no visible global function definition for
  ‘colorRampPalette’
qaProcess.ECDFPlot: no visible global function definition for
  ‘brewer.pal’
qaProcess.ECDFPlot: no visible global function definition for ‘ppoints’
qaProcess.ECDFPlot: no visible global function definition for
  ‘quantile’
qaProcess.ECDFPlot: no visible global function definition for ‘xyplot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible global function definition for
  ‘simpleKey’
qaProcess.ECDFPlot: no visible global function definition for
  ‘KLdist.matrix’
qaProcess.ECDFPlot: no visible global function definition for
  ‘ecdfplot’
qaProcess.ECDFPlot: no visible global function definition for
  ‘densityplot’
qaProcess.ECDFPlot : <anonymous>: no visible binding for global
  variable ‘panel.xyplot’
qaProcess.ECDFPlot : <anonymous>: no visible global function definition
  for ‘trellis.panelArgs’
qaProcess.ECDFPlot: no visible global function definition for ‘dev.off’
qaProcess.ECDFPlot: no visible global function definition for
  ‘calout.detect’
qaProcess.KLDistPlot: no visible global function definition for
  ‘colorRampPalette’
qaProcess.KLDistPlot: no visible global function definition for
  ‘brewer.pal’
qaProcess.KLDistPlot: no visible global function definition for
  ‘KLdist.matrix’
qaProcess.KLDistPlot: no visible global function definition for
  ‘levelplot’
qaProcess.KLDistPlot: no visible global function definition for
  ‘dev.off’
qaProcess.KLDistPlot: no visible global function definition for
  ‘calout.detect’
qaProcess.cellnumber: no visible global function definition for ‘par’
qaProcess.cellnumber: no visible global function definition for
  ‘barplot’
qaProcess.cellnumber: no visible global function definition for
  ‘abline’
qaProcess.cellnumber: no visible global function definition for ‘text’
qaProcess.cellnumber: no visible global function definition for
  ‘dev.off’
qaProcess.marginevents: no visible global function definition for
  ‘colorRampPalette’
qaProcess.marginevents: no visible global function definition for
  ‘levelplot’
qaProcess.marginevents: no visible global function definition for
  ‘dev.off’
qaProcess.marginevents: no visible global function definition for ‘par’
qaProcess.marginevents: no visible global function definition for
  ‘density’
qaProcess.marginevents: no visible global function definition for
  ‘extendrange’
qaProcess.marginevents: no visible global function definition for
  ‘polygon’
qaProcess.marginevents: no visible global function definition for
  ‘text’
qaProcess.timeflow: no visible global function definition for ‘median’
qaProcess.timeflow: no visible global function definition for
  ‘timeLinePlot’
qaProcess.timeflow: no visible global function definition for ‘text’
qaProcess.timeflow: no visible global function definition for ‘dev.off’
qaProcess.timeline: no visible global function definition for ‘median’
qaProcess.timeline: no visible global function definition for
  ‘timeLinePlot’
qaProcess.timeline: no visible global function definition for ‘text’
qaProcess.timeline: no visible global function definition for ‘dev.off’
writeQATextReport: no visible global function definition for
  ‘write.table’
outliers,flowSet: no visible binding for global variable ‘variance’
Undefined global functions or variables:
  Aliquot IQR KLdist.matrix abline barchart barplot brewer.pal
  calout.detect chisq.out.test colorRampPalette density densityplot
  dev.off dixon.test ecdfplot extendrange grubbs.test levelplot listLen
  median panel.xyplot par pcout polygon ppoints quantile sd simpleKey
  text timeLinePlot trellis.panelArgs var variance warpSet write.table
  xyplot
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "extendrange")
  importFrom("graphics", "abline", "barplot", "par", "polygon", "text")
  importFrom("stats", "IQR", "density", "median", "ppoints", "quantile",
             "sd", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'qaProcess.timeflow.Rd':
  ‘[flowViz:timeLinePlot-methods]{timeLinePlot}’

Missing link or links in documentation object 'qaProcess.timeline.Rd':
  ‘[flowViz:timeLinePlot-methods]{timeLinePlot}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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
qaProcess.2DStatsPlot  17.997  0.825  19.359
qaProcess.KLDistPlot   12.481  0.417  12.993
qaProcess.DensityPlot  12.408  0.445  12.994
qaProcess.ECDFPlot     11.596  0.424  12.159
qaProcess.BoundaryPlot 10.394  0.426  10.918
* 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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowQ.Rcheck/00check.log’
for details.

flowQ.Rcheck/00install.out:

* installing *source* package ‘flowQ’ ...
** 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 (flowQ)

flowQ.Rcheck/flowQ-Ex.timings:

nameusersystemelapsed
aggregatorList-class0.0020.0000.002
binaryAggregator-class0.0010.0000.002
discreteAggregator-class0.0010.0000.001
evaluateProcess0.0010.0000.001
factorAggregator-class0.0010.0000.001
flowQ-package0.0010.0010.001
numericAggregator-class0.0010.0000.001
outlier-class0.0010.0000.001
outlierResult-class0.0000.0000.001
qaAggregator-class0.0010.0010.001
qaGraph-class0.0010.0000.001
qaGraphList-class0.0000.0000.001
qaProcess-class0.0010.0010.002
qaProcess.2DStatsPlot17.997 0.82519.359
qaProcess.BoundaryPlot10.394 0.42610.918
qaProcess.DensityPlot12.408 0.44512.994
qaProcess.ECDFPlot11.596 0.42412.159
qaProcess.KLDistPlot12.481 0.41712.993
qaProcess.cellnumber0.0000.0000.001
qaProcess.marginevents0.0010.0000.001
qaProcess.timeflow0.0010.0000.000
qaProcess.timeline0.0000.0000.001
qaProcessFrame-class0.0010.0010.002
qaReport0.0010.0000.001
rangeAggregator-class0.0010.0000.002
stringAggregator-class0.0010.0000.001
txtFormatQAObject3.1470.5263.768
writeQAReport0.0000.0000.001
writeQATextReport0.0000.0000.001