Back to Multiple platform build/check report for BioC 3.7
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CRImage on malbec2

This page was generated on 2018-10-17 08:23:16 -0400 (Wed, 17 Oct 2018).

Package 320/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.28.0
Henrik Failmezger , Yinyin Yuan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CRImage
Branch: RELEASE_3_7
Last Commit: 9a462b6
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CRImage
Version: 1.28.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CRImage.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CRImage_1.28.0.tar.gz
StartedAt: 2018-10-15 23:32:41 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:33:52 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 71.2 seconds
RetCode: 0
Status:  OK 
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:CRImage.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings CRImage_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/CRImage.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 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-3.7-bioc/meat/CRImage.Rcheck/00check.log’
for details.



Installation output

CRImage.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL CRImage
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘CRImage’ ...
** 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
* DONE (CRImage)

Tests output


Example timings

CRImage.Rcheck/CRImage-Ex.timings

nameusersystemelapsed
CRImage-package0.2360.0120.349
SauvolaThreshold0.4080.0400.466
calculateCellularity4.0440.0644.115
calculateMeanStdTarget1.1560.0121.170
calculateOtsu0.0840.0160.102
classifyCells2.2080.0122.221
colorCorrection0.8320.0040.837
convertHSVToRGB0.3880.0000.391
convertLABToRGB0.3840.0000.386
convertRGBToHSV2.2720.0282.304
convertRGBToLAB0.4960.0000.497
correctCopyNumber0.0960.0000.098
createBinaryImage1.6400.0081.652
createClassifier0.1720.0000.173
labelCells000
plotCorrectedCN0.1080.0000.106
processAperio0.0160.0000.026
segmentImage0.0000.0000.001