Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:06:25 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CRImage on tokay2


To the developers/maintainers of the CRImage package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CRImage.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 415/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CRImage 1.42.0  (landing page)
Henrik Failmezger , Yinyin Yuan
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/CRImage
git_branch: RELEASE_3_14
git_last_commit: 7a30984
git_last_commit_date: 2021-10-26 11:57:17 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CRImage
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRImage_1.42.0.tar.gz
StartedAt: 2022-01-25 17:57:53 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 17:59:54 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 121.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CRImage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CRImage.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CRImage_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRImage.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.42.0'
* 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  5.8Mb
  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 '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 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",
             "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
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CRImage.Rcheck/00check.log'
for details.



Installation output

CRImage.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CRImage_1.42.0.tar.gz && rm -rf CRImage.buildbin-libdir && mkdir CRImage.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CRImage.buildbin-libdir CRImage_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CRImage_1.42.0.zip && rm CRImage_1.42.0.tar.gz CRImage_1.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 14 6453k   14  923k    0     0  2277k      0  0:00:02 --:--:--  0:00:02 2275k
 94 6453k   94 6119k    0     0  4411k      0  0:00:01  0:00:01 --:--:-- 4412k
100 6453k  100 6453k    0     0  4506k      0  0:00:01  0:00:01 --:--:-- 4506k

install for i386

* installing *source* package 'CRImage' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CRImage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CRImage' as CRImage_1.42.0.zip
* DONE (CRImage)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CRImage' successfully unpacked and MD5 sums checked

Tests output


Example timings

CRImage.Rcheck/examples_i386/CRImage-Ex.timings

nameusersystemelapsed
CRImage-package0.450.000.56
SauvolaThreshold0.060.020.13
calculateCellularity3.390.343.78
calculateMeanStdTarget0.710.301.03
calculateOtsu0.060.010.08
classifyCells2.110.252.36
colorCorrection0.620.110.75
convertHSVToRGB0.330.070.39
convertLABToRGB0.250.070.33
convertRGBToHSV2.640.182.81
convertRGBToLAB0.250.110.36
correctCopyNumber0.080.000.08
createBinaryImage0.670.140.83
createClassifier0.330.000.33
labelCells000
plotCorrectedCN0.160.000.15
processAperio0.030.000.17
segmentImage000

CRImage.Rcheck/examples_x64/CRImage-Ex.timings

nameusersystemelapsed
CRImage-package0.270.000.27
SauvolaThreshold0.250.000.25
calculateCellularity2.620.362.98
calculateMeanStdTarget0.770.180.96
calculateOtsu0.050.020.06
classifyCells1.940.312.25
colorCorrection0.730.200.94
convertHSVToRGB0.320.100.41
convertLABToRGB0.320.060.39
convertRGBToHSV2.180.172.34
convertRGBToLAB0.540.080.63
correctCopyNumber0.080.000.08
createBinaryImage0.520.110.62
createClassifier0.170.000.17
labelCells000
plotCorrectedCN0.100.000.09
processAperio0.010.000.02
segmentImage000