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CHECK report for Cardinal on tokay1

This page was generated on 2018-04-12 13:25:41 -0400 (Thu, 12 Apr 2018).

Package 181/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 1.10.0
Kylie A. Bemis
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/Cardinal
Branch: RELEASE_3_6
Last Commit: a8d7a0c
Last Changed Date: 2017-10-30 12:40:48 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Cardinal
Version: 1.10.0
Command: rm -rf Cardinal.buildbin-libdir Cardinal.Rcheck && mkdir Cardinal.buildbin-libdir Cardinal.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Cardinal.buildbin-libdir Cardinal_1.10.0.tar.gz >Cardinal.Rcheck\00install.out 2>&1 && cp Cardinal.Rcheck\00install.out Cardinal-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Cardinal.buildbin-libdir --install="check:Cardinal-install.out" --force-multiarch --no-vignettes --timings Cardinal_1.10.0.tar.gz
StartedAt: 2018-04-11 22:41:25 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:45:21 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 236.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Cardinal.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf Cardinal.buildbin-libdir Cardinal.Rcheck && mkdir Cardinal.buildbin-libdir Cardinal.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Cardinal.buildbin-libdir Cardinal_1.10.0.tar.gz >Cardinal.Rcheck\00install.out 2>&1 && cp Cardinal.Rcheck\00install.out Cardinal-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Cardinal.buildbin-libdir --install="check:Cardinal-install.out" --force-multiarch --no-vignettes --timings Cardinal_1.10.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Cardinal/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Cardinal' version '1.10.0'
* 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 'Cardinal' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/IAnnotatedDataFrame-class.Rd:100: missing file link 'AnnotatedDataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/MSImageData-class.Rd:53: missing file link 'peakAlign'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:46: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:47: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:82: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:83: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:84: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:35: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:55: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:56: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:44: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:45: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:75: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:76: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:77: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'spatialKMeans'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:88: missing file link 'iSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:89: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:90: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:91: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:92: missing file link 'spatialKMeans'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:93: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:44: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:58: missing file link 'normalize'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:59: missing file link 'smoothSignal'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:60: missing file link 'reduceBaseline'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:61: missing file link 'peakPick'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:62: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/coregister-methods.Rd:30: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:38: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:39: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:40: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/normalize-methods.Rd:42: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/normalize-methods.Rd:52: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:59: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:69: missing file link 'peakPick'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:70: missing file link 'peakFilter'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:71: missing file link 'reduceDimension'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:72: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:41: missing file link 'featureApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:51: missing file link 'peakPick'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:52: missing file link 'peakAlign'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:53: missing file link 'reduceDimension'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:54: missing file link 'featureApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:59: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:72: missing file link 'peakAlign'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:73: missing file link 'peakFilter'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:74: missing file link 'reduceDimension'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:75: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:46: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:47: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:48: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceBaseline-methods.Rd:44: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceBaseline-methods.Rd:54: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:73: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:83: missing file link 'peakPick'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:84: missing file link 'peakAlign'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:85: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:10: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:22: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:24: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:25: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:26: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:36: missing file link 'image'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/smoothSignal-methods.R.rd:53: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/smoothSignal-methods.R.rd:63: missing file link 'pixelApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialKMeans-methods.Rd:59: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialShrunkenCentroids-methods.Rd:43: missing file link 'spatialShrunkenCentroids'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialShrunkenCentroids-methods.Rd:74: missing file link 'spatialKMeans'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/standardizeSamples-methods.Rd:37: missing file link 'featureApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/standardizeSamples-methods.Rd:47: missing file link 'featureApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:66: missing file link 'PCA'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:67: missing file link 'PLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:68: missing file link 'OPLS'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:69: missing file link 'spatialKMeans'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:70: missing file link 'spatialShrunkenCentroids'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calculateSpatialDiscriminantScores: no visible global function
  definition for 'median'
.console: no visible global function definition for 'flush.console'
.onAttach: no visible global function definition for 'packageVersion'
.plot.gridsearch: no visible global function definition for 'points'
.plot.gridsearch: no visible global function definition for 'abline'
.plot.gridsearch: no visible global function definition for 'legend'
.setup.layout: no visible global function definition for 'par'
.spatialKMeans: no visible global function definition for 'kmeans'
.spatialShrunkenCentroids.fit: no visible global function definition
  for 'median'
.spatialShrunkenCentroids.predict: no visible global function
  definition for 'median'
alpha.colors: no visible global function definition for 'col2rgb'
alpha.colors: no visible global function definition for 'rgb'
contrast.enhance.histogram: no visible global function definition for
  'quantile'
contrast.enhance.suppression: no visible global function definition for
  'quantile'
generateSpectrum: no visible global function definition for 'runif'
generateSpectrum: no visible global function definition for 'rnorm'
generateSpectrum : <anonymous>: no visible global function definition
  for 'dnorm'
gradient.colors: no visible global function definition for 'colorRamp'
gradient.colors : <anonymous>: no visible binding for global variable
  'rgb'
image3d: no visible global function definition for 'persp'
image3d: no visible global function definition for 'points'
image3d: no visible global function definition for 'trans3d'
intensity.colors: no visible global function definition for 'rainbow'
intensity.colors: no visible global function definition for 'colorRamp'
intensity.colors: no visible global function definition for 'col2rgb'
intensity.colors : <anonymous>: no visible binding for global variable
  'rgb'
intensity.colors2: no visible global function definition for 'rainbow'
interp.surface: no visible global function definition for 'approx'
normalize.do: no visible global function definition for 'lines'
peakAlign.do: no visible global function definition for 'abline'
peakPick.adaptive: no visible global function definition for
  'smooth.spline'
peakPick.adaptive: no visible global function definition for 'median'
peakPick.do: no visible global function definition for 'lines'
peakPick.limpic: no visible global function definition for 'median'
peakPick.limpic: no visible global function definition for 'quantile'
reduceBaseline.do: no visible global function definition for 'lines'
reduceBaseline.median: no visible global function definition for
  'smooth.spline'
reduceDimension.do: no visible global function definition for 'points'
reduceDimension.do: no visible global function definition for 'lines'
risk.colors: no visible global function definition for 'colorRamp'
risk.colors : <anonymous>: no visible binding for global variable 'rgb'
smoothSignal.do: no visible global function definition for 'lines'
smoothSignal.gaussian: no visible global function definition for
  'dnorm'
smoothSignal.ma: no visible global function definition for 'filter'
batchProcess,MSImageSet : <anonymous>: no visible binding for global
  variable '.Index'
image,ResultSet: no visible global function definition for 'rainbow'
image,ResultSet: no visible global function definition for 'as.formula'
image,SImageSet: no visible global function definition for 'rainbow'
image,SImageSet: no visible global function definition for 'as.formula'
image,SImageSet: no visible global function definition for 'legend'
image,SImageSet: no visible global function definition for 'rgb'
initialize,MSImageProcess: no visible global function definition for
  'packageDescription'
normalize,MSImageSet : <anonymous>: no visible binding for global
  variable '.Index'
peakAlign,MSImageSet-numeric : <anonymous>: no visible binding for
  global variable '.Index'
peakPick,MSImageSet : <anonymous>: no visible binding for global
  variable '.Index'
plot,ResultSet-missing: no visible global function definition for
  'rainbow'
plot,ResultSet-missing: no visible global function definition for
  'as.formula'
plot,SImageSet-missing: no visible global function definition for
  'as.formula'
plot,SImageSet-missing: no visible global function definition for
  'abline'
plot,SImageSet-missing: no visible global function definition for
  'points'
plot,SImageSet-missing: no visible global function definition for
  'legend'
plot,SImageSet-missing: no visible global function definition for 'rgb'
reduceBaseline,MSImageSet : <anonymous>: no visible binding for global
  variable '.Index'
reduceDimension,MSImageSet-missing : <anonymous>: no visible binding
  for global variable '.Index'
select,SImageSet: no visible global function definition for 'locator'
show,ImageData: no visible global function definition for 'object.size'
smoothSignal,MSImageSet : <anonymous>: no visible binding for global
  variable '.Index'
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
  function definition for 'pt'
summary,SpatialShrunkenCentroids : <anonymous>: no visible global
  function definition for 'p.adjust'
summary,iSet : <anonymous>: no visible global function definition for
  'object.size'
summary,iSet: no visible global function definition for 'object.size'
Undefined global functions or variables:
  .Index abline approx as.formula col2rgb colorRamp dnorm filter
  flush.console kmeans legend lines locator median object.size p.adjust
  packageDescription packageVersion par persp points pt quantile
  rainbow rgb rnorm runif smooth.spline trans3d
Consider adding
  importFrom("grDevices", "col2rgb", "colorRamp", "rainbow", "rgb",
             "trans3d")
  importFrom("graphics", "abline", "legend", "lines", "locator", "par",
             "persp", "points")
  importFrom("stats", "approx", "as.formula", "dnorm", "filter",
             "kmeans", "median", "p.adjust", "pt", "quantile", "rnorm",
             "runif", "smooth.spline")
  importFrom("utils", "flush.console", "object.size",
             "packageDescription", "packageVersion")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/i386/Cardinal.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.Rcheck/00check.log'
for details.

Installation output

Cardinal.Rcheck/00install.out


install for i386

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fastmap.c -o fastmap.o
fastmap.c: In function 'choose_distant_objects':
fastmap.c:59:24: warning: 'o_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:1452:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:1458:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c readAnalyze.cpp -o readAnalyze.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c readImzML.cpp -o readImzML.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Cardinal'
    finding HTML links ... done
    Binmat-class                            html  
    finding level-2 HTML links ... done

    Cardinal-package                        html  
    Hashmat-class                           html  
    IAnnotatedDataFrame-class               html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/IAnnotatedDataFrame-class.Rd:100: missing file link 'AnnotatedDataFrame'
    ImageData-class                         html  
    MIAPE-Imaging-class                     html  
    MSImageData-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/MSImageData-class.Rd:53: missing file link 'peakAlign'
    MSImageProcess-class                    html  
    MSImageSet-class                        html  
    OPLS-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:46: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:47: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:82: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:83: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/OPLS-methods.Rd:84: missing file link 'spatialShrunkenCentroids'
    PCA-methods                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:35: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:55: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PCA-methods.Rd:56: missing file link 'PLS'
    PLS-methods                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:44: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:45: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:75: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:76: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/PLS-methods.Rd:77: missing file link 'spatialShrunkenCentroids'
    ResultSet-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'spatialKMeans'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:28: missing file link 'spatialShrunkenCentroids'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:88: missing file link 'iSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:89: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:90: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:91: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:92: missing file link 'spatialKMeans'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/ResultSet-class.Rd:93: missing file link 'spatialShrunkenCentroids'
    SImageData-class                        html  
    SImageSet-class                         html  
    batchProcess-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:44: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:58: missing file link 'normalize'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:59: missing file link 'smoothSignal'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:60: missing file link 'reduceBaseline'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:61: missing file link 'peakPick'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/batchProcess-methods.Rd:62: missing file link 'pixelApply'
    colors-functions                        html  
    coord-methods                           html  
    coregister-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/coregister-methods.Rd:30: missing file link 'spatialShrunkenCentroids'
    cvApply-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:38: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:39: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/cvApply-methods.Rd:40: missing file link 'spatialShrunkenCentroids'
    generateImage                           html  
    generateSpectrum                        html  
    iSet-class                              html  
    image-methods                           html  
    imageData-methods                       html  
    mz-methods                              html  
    normalize-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/normalize-methods.Rd:42: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/normalize-methods.Rd:52: missing file link 'pixelApply'
    peakAlign-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:59: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:69: missing file link 'peakPick'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:70: missing file link 'peakFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:71: missing file link 'reduceDimension'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakAlign-methods.Rd:72: missing file link 'pixelApply'
    peakFilter-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:41: missing file link 'featureApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:51: missing file link 'peakPick'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:52: missing file link 'peakAlign'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:53: missing file link 'reduceDimension'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakFilter-methods.Rd:54: missing file link 'featureApply'
    peakPick-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:59: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:72: missing file link 'peakAlign'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:73: missing file link 'peakFilter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:74: missing file link 'reduceDimension'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/peakPick-methods.Rd:75: missing file link 'pixelApply'
    pixelApply-methods                      html  
    pixelData-methods                       html  
    pixelNames-methods                      html  
    pixels-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:46: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:47: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/pixels-methods.Rd:48: missing file link 'spatialShrunkenCentroids'
    plot-methods                            html  
    processingData-methods                  html  
    readMSIData                             html  
    reduceBaseline-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceBaseline-methods.Rd:44: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceBaseline-methods.Rd:54: missing file link 'pixelApply'
    reduceDimension-methods                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:73: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:83: missing file link 'peakPick'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:84: missing file link 'peakAlign'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/reduceDimension-methods.Rd:85: missing file link 'pixelApply'
    select-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:10: missing file link 'image'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:22: missing file link 'image'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:24: missing file link 'image'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:25: missing file link 'image'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:26: missing file link 'image'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/select-methods.Rd:36: missing file link 'image'
    smoothSignal-methods.R                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/smoothSignal-methods.R.rd:53: missing file link 'pixelApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/smoothSignal-methods.R.rd:63: missing file link 'pixelApply'
    spatialKMeans-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialKMeans-methods.Rd:59: missing file link 'spatialShrunkenCentroids'
    spatialShrunkenCentroids-methods        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialShrunkenCentroids-methods.Rd:43: missing file link 'spatialShrunkenCentroids'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/spatialShrunkenCentroids-methods.Rd:74: missing file link 'spatialKMeans'
    standardizeSamples-methods              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/standardizeSamples-methods.Rd:37: missing file link 'featureApply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/standardizeSamples-methods.Rd:47: missing file link 'featureApply'
    topLabels-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:66: missing file link 'PCA'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:67: missing file link 'PLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:68: missing file link 'OPLS'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:69: missing file link 'spatialKMeans'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp6RUFVT/R.INSTALL2674ad875d6/Cardinal/man/topLabels-methods.Rd:70: missing file link 'spatialShrunkenCentroids'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Cardinal' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dynamicAlign.c -o dynamicAlign.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fastmap.c -o fastmap.o
fastmap.c: In function 'choose_distant_objects':
fastmap.c:59:24: warning: 'o_b' may be used uninitialized in this function [-Wmaybe-uninitialized]
  pivot_objects->b[col] = o_b;
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c localMaxima.c -o localMaxima.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pugixml.cpp -o pugixml.o
pugixml.cpp:1452:18: warning: 'size_t pugi::impl::{anonymous}::as_utf8_begin(const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN size_t as_utf8_begin(const wchar_t* str, size_t length)
                  ^
pugixml.cpp:1458:16: warning: 'void pugi::impl::{anonymous}::as_utf8_end(char*, size_t, const wchar_t*, size_t)' defined but not used [-Wunused-function]
  PUGI__FN void as_utf8_end(char* buffer, size_t size, const wchar_t* str, size_t length)
                ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c readAnalyze.cpp -o readAnalyze.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c readImzML.cpp -o readImzML.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spatial.c -o spatial.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Cardinal.dll tmp.def dynamicAlign.o fastmap.o localMaxima.o pugixml.o readAnalyze.o readImzML.o smooth.o spatial.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/Cardinal.buildbin-libdir/Cardinal/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Cardinal' as Cardinal_1.10.0.zip
* DONE (Cardinal)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Cardinal.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: matter
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following objects are masked from 'package:base':

    apply, scale

Loading required package: ProtGenerics
Welcome to Cardinal (version 1.10.0)

    To get started, view the introductory vignettes with
    'browseVignettes("Cardinal")'.

> 
> test_check("Cardinal")
== testthat results  ===========================================================
OK: 229 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  25.87    0.50   26.35

Cardinal.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Cardinal)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: matter
Loading required package: biglm
Loading required package: DBI

Attaching package: 'matter'

The following objects are masked from 'package:base':

    apply, scale

Loading required package: ProtGenerics
Welcome to Cardinal (version 1.10.0)

    To get started, view the introductory vignettes with
    'browseVignettes("Cardinal")'.

> 
> test_check("Cardinal")
== testthat results  ===========================================================
OK: 229 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.51    0.12   27.62

Example timings

Cardinal.Rcheck/examples_i386/Cardinal-Ex.timings

nameusersystemelapsed
Binmat-class000
Hashmat-class0.250.010.27
IAnnotatedDataFrame-class0.10.00.1
ImageData-class0.010.020.03
MIAPE-Imaging-class0.020.000.02
MSImageData-class0.20.00.2
MSImageProcess-class000
MSImageSet-class0.220.000.22
OPLS-methods0.150.000.15
PCA-methods0.070.000.21
PLS-methods0.060.000.06
SImageData-class0.080.000.08
SImageSet-class0.080.000.08
batchProcess-methods0.810.000.81
colors-functions1.080.001.08
generateImage0.340.020.36
generateSpectrum0.050.000.04
iSet-class0.030.000.03
image-methods0.550.000.55
normalize-methods0.100.000.11
peakAlign-methods0.350.000.34
peakFilter-methods0.330.000.33
peakPick-methods0.110.000.11
pixelApply-methods0.030.000.03
pixels-methods0.080.000.08
plot-methods0.580.000.57
reduceBaseline-methods0.090.000.10
reduceDimension-methods0.110.000.11
smoothSignal-methods.R0.080.000.08
spatialKMeans-methods0.50.00.5
spatialShrunkenCentroids-methods1.390.001.39
standardizeSamples-methods0.360.000.36
topLabels-methods0.840.000.84

Cardinal.Rcheck/examples_x64/Cardinal-Ex.timings

nameusersystemelapsed
Binmat-class000
Hashmat-class0.830.010.85
IAnnotatedDataFrame-class0.120.000.13
ImageData-class0.030.000.03
MIAPE-Imaging-class000
MSImageData-class0.280.020.30
MSImageProcess-class000
MSImageSet-class0.30.00.3
OPLS-methods0.220.000.22
PCA-methods0.070.000.79
PLS-methods0.080.000.08
SImageData-class0.110.000.11
SImageSet-class0.080.000.08
batchProcess-methods0.720.000.72
colors-functions1.370.001.37
generateImage0.410.000.41
generateSpectrum0.050.000.05
iSet-class0.040.000.04
image-methods0.660.000.66
normalize-methods0.130.000.12
peakAlign-methods0.430.000.44
peakFilter-methods0.440.000.44
peakPick-methods0.140.000.14
pixelApply-methods0.050.000.05
pixels-methods0.110.000.11
plot-methods0.830.000.82
reduceBaseline-methods0.140.000.14
reduceDimension-methods0.140.000.14
smoothSignal-methods.R0.130.000.13
spatialKMeans-methods0.610.000.60
spatialShrunkenCentroids-methods1.810.001.82
standardizeSamples-methods0.50.00.5
topLabels-methods0.970.000.97