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BioC 3.5: CHECK report for CRImage on veracruz2

This page was generated on 2017-08-16 13:29:02 -0400 (Wed, 16 Aug 2017).

Package 293/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.24.0
Henrik Failmezger , Yinyin Yuan
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CRImage
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CRImage
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRImage_1.24.0.tar.gz
StartedAt: 2017-08-16 01:32:30 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:34:20 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 110.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRImage_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CRImage.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRImage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRImage’ version ‘1.24.0’
* 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 ‘CRImage’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' calls to packages already attached by Depends:
  ‘DNAcopy’ ‘aCGH’
  Please remove these calls from your code.
':::' call which should be '::': ‘aCGH:::combine.func’
  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
Phansalkar_threshold: no visible global function definition for ‘sd’
SauvolaThreshold: no visible global function definition for ‘sd’
calculateMeanStdTarget: no visible global function definition for ‘sd’
calculateOtsu: no visible global function definition for ‘optimize’
classificationAperio: no visible global function definition for
  ‘write.table’
classificationAperio: no visible global function definition for
  ‘read.table’
classifyCells: no visible global function definition for ‘predict’
classifyPen: no visible global function definition for ‘predict’
colorCorrection: no visible global function definition for ‘sd’
correctCopyNumber : Myansari.test.default: no visible global function
  definition for ‘complete.cases’
correctCopyNumber : Myansari.test.default: no visible global function
  definition for ‘pnorm’
correctCopyNumber : Myansari.test.default : ccia: no visible global
  function definition for ‘qnorm’
correctCopyNumber : Myansari.test.default : ccia: no visible global
  function definition for ‘uniroot’
correctCopyNumber : Myansari.test.default: no visible global function
  definition for ‘uniroot’
correctCopyNumber: no visible global function definition for ‘quantile’
correctCopyNumber: no visible global function definition for ‘median’
determineCellularity: no visible global function definition for
  ‘colorRampPalette’
determineCellularity: no visible global function definition for
  ‘col2rgb’
findSlices: no visible global function definition for ‘cutree’
findSlices: no visible global function definition for ‘hclust’
findSlices: no visible global function definition for ‘dist’
findSlices: no visible global function definition for ‘col2rgb’
kernelSmoother: no visible global function definition for ‘dist’
labelCells: no visible global function definition for ‘points’
labelCells: no visible global function definition for ‘title’
labelCells : refresh: no visible global function definition for
  ‘points’
labelCells : refresh: no visible global function definition for ‘title’
labelCells : refresh: no visible global function definition for
  ‘write.table’
labelCells : keydown: no visible global function definition for
  ‘write.table’
labelCells : keydown: no visible global function definition for ‘title’
labelCells : dragmousedown: no visible global function definition for
  ‘grconvertX’
labelCells : dragmousedown: no visible global function definition for
  ‘grconvertY’
labelCells : dragmousemove: no visible global function definition for
  ‘grconvertX’
labelCells : dragmousemove: no visible global function definition for
  ‘grconvertY’
labelCells : dragmousemove: no visible global function definition for
  ‘lines’
labelCells : dragmouseup: no visible global function definition for
  ‘chull’
labelCells : dragmouseup: no visible global function definition for
  ‘grconvertX’
labelCells : dragmouseup: no visible global function definition for
  ‘grconvertY’
labelCells: no visible global function definition for
  ‘setGraphicsEventHandlers’
labelCells: no visible global function definition for
  ‘getGraphicsEvent’
numberOfNeighbors: no visible global function definition for ‘dist’
plotCorrectedCN: no visible global function definition for ‘par’
plotCorrectedCN: no visible global function definition for ‘plot’
plotCorrectedCN: no visible global function definition for ‘segments’
plotCorrectedCN: no visible global function definition for ‘title’
plotImage: no visible global function definition for ‘grey’
plotImage: no visible global function definition for ‘rgb’
processAperio: no visible global function definition for ‘write.table’
processAperio: no visible global function definition for ‘col2rgb’
segmentStructures: no visible global function definition for ‘predict’
Undefined global functions or variables:
  chull col2rgb colorRampPalette complete.cases cutree dist
  getGraphicsEvent grconvertX grconvertY grey hclust lines median
  optimize par plot pnorm points predict qnorm quantile read.table rgb
  sd segments setGraphicsEventHandlers title uniroot write.table
Consider adding
  importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
             "getGraphicsEvent", "grey", "rgb",
             "setGraphicsEventHandlers")
  importFrom("graphics", "grconvertX", "grconvertY", "lines", "par",
             "plot", "points", "segments", "title")
  importFrom("stats", "complete.cases", "cutree", "dist", "hclust",
             "median", "optimize", "pnorm", "predict", "qnorm",
             "quantile", "sd", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 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
calculateCellularity 6.005  0.947   7.135
classifyCells        5.165  0.807   6.201
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/CRImage.Rcheck/00check.log’
for details.


CRImage.Rcheck/00install.out:

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

CRImage.Rcheck/CRImage-Ex.timings:

nameusersystemelapsed
CRImage-package0.2680.0140.294
SauvolaThreshold0.9290.0491.004
calculateCellularity6.0050.9477.135
calculateMeanStdTarget1.5290.6072.214
calculateOtsu0.3250.0850.423
classifyCells5.1650.8076.201
colorCorrection1.7740.5782.439
convertHSVToRGB0.6120.1660.834
convertLABToRGB0.4480.1540.617
convertRGBToHSV3.7930.1204.033
convertRGBToLAB0.5770.1690.771
correctCopyNumber0.4420.0070.469
createBinaryImage1.4330.5442.010
createClassifier0.2190.0070.235
labelCells0.0010.0000.001
plotCorrectedCN1.1710.0341.233
processAperio0.0170.0000.017
segmentImage0.0010.0000.001