Package: CRImage

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CRImage_1.28.0.tar.gz

StartedAt: 2018-10-17 01:22:43 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:25:20 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 157.6 seconds

RetCode: 0

Status:  OK

CheckDir: CRImage.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CRImage_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CRImage.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CRImage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CRImage' version '1.28.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 5.62   1.67    7.45
classifyCells        4.28   1.34    5.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
calculateCellularity 6.28   1.70    7.98
classifyCells        4.36   1.58    5.94
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/CRImage.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CRImage_1.28.0.tar.gz && rm -rf CRImage.buildbin-libdir && mkdir CRImage.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CRImage.buildbin-libdir CRImage_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CRImage_1.28.0.zip && rm CRImage_1.28.0.tar.gz CRImage_1.28.0.zip
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100 6442k  100 6442k    0     0  44.6M      0 --:--:-- --:--:-- --:--:-- 46.9M

install for i386

* installing *source* package 'CRImage' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CRImage'
    finding HTML links ... done
    CRImage-internal                        html  
    CRImage-package                         html  
    SauvolaThreshold                        html  
    calculateCellularity                    html  
    calculateMeanStdTarget                  html  
    calculateOtsu                           html  
    classifyCells                           html  
    colorCorrection                         html  
    convertHSVToRGB                         html  
    convertLABToRGB                         html  
    convertRGBToHSV                         html  
    convertRGBToLAB                         html  
    correctCopyNumber                       html  
    createBinaryImage                       html  
    createClassifier                        html  
    labelCells                              html  
    plotCorrectedCN                         html  
    processAperio                           html  
    segmentImage                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CRImage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRImage' as CRImage_1.28.0.zip
* DONE (CRImage)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CRImage' successfully unpacked and MD5 sums checked
In R CMD INSTALL