Package: CRImage

Version: 1.31.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CRImage.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CRImage_1.31.0.tar.gz

StartedAt: 2019-04-08 23:46:24 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:47:50 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 86.2 seconds

RetCode: 0

Status:  OK

CheckDir: CRImage.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CRImage.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CRImage_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CRImage.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.31.0’
* 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  5.7Mb
  sub-directories of 1Mb or more:
    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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.9-bioc/meat/CRImage.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CRImage
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CRImage’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CRImage)

name	user	system	elapsed
CRImage-package	0.292	0.028	0.388
SauvolaThreshold	0.066	0.016	0.099
calculateCellularity	3.347	0.088	3.455
calculateMeanStdTarget	0.731	0.000	0.742
calculateOtsu	0.054	0.000	0.055
classifyCells	2.345	0.011	2.358
colorCorrection	0.837	0.004	0.842
convertHSVToRGB	0.157	0.003	0.160
convertLABToRGB	0.367	0.000	0.367
convertRGBToHSV	3.627	0.012	3.640
convertRGBToLAB	0.523	0.012	0.535
correctCopyNumber	0.126	0.000	0.126
createBinaryImage	0.719	0.008	0.728
createClassifier	0.253	0.000	0.253
labelCells	0	0	0
plotCorrectedCN	0.147	0.002	0.149
processAperio	0.014	0.008	0.043
segmentImage	0	0	0