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CHECK report for BiocGenerics on tokay1

This page was generated on 2018-04-12 13:21:26 -0400 (Thu, 12 Apr 2018).

Package 123/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.24.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiocGenerics
Branch: RELEASE_3_6
Last Commit: 3db111e
Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocGenerics
Version: 0.24.0
Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.24.0.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.24.0.tar.gz
StartedAt: 2018-04-11 22:28:59 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:30:54 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 115.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.24.0.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocGenerics.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 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.24.0'
* 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 'BiocGenerics' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:31: missing file link 'rbind'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:36: missing file link 'anyDuplicated'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:41: missing file link 'pmax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:42: missing file link 'pmin'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:43: missing file link 'pmax.int'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:44: missing file link 'pmin.int'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:47: missing file link 'Reduce'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:48: missing file link 'Filter'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:49: missing file link 'Find'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:50: missing file link 'Map'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:51: missing file link 'Position'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:54: missing file link 'mget'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:57: missing file link 'grepl'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:62: missing file link 'sapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:71: missing file link 'ncol'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:72: missing file link 'NROW'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:73: missing file link 'NCOL'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:81: missing file link 'rep.int'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:83: missing file link 'rownames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:84: missing file link 'rownames<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:85: missing file link 'colnames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:86: missing file link 'colnames<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:89: missing file link 'union'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:90: missing file link 'intersect'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:91: missing file link 'setdiff'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:96: missing file link 'start<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:97: missing file link 'end'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:98: missing file link 'end<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:99: missing file link 'width'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:100: missing file link 'width<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:138: missing file link 'clusterCall'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:140: missing file link 'clusterApplyLB'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:141: missing file link 'clusterEvalQ'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:142: missing file link 'clusterExport'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:143: missing file link 'clusterMap'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:144: missing file link 'clusterSplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:145: missing file link 'parLapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:146: missing file link 'parSapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:147: missing file link 'parApply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:148: missing file link 'parRapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:149: missing file link 'parCapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:150: missing file link 'parLapplyLB'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:151: missing file link 'parSapplyLB'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:158: missing file link 'annotation<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:163: missing file link 'dbfile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:171: missing file link 'organism'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:172: missing file link 'organism<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:173: missing file link 'species'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:174: missing file link 'species<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:181: missing file link 'score<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:184: missing file link 'strand<-'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:185: missing file link 'invertStrand'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:224: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:18: missing file link 'pmax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:38: missing file link 'pmax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:44: missing file link 'pmax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:53: missing file link 'pmax'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:59: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:62: missing file link 'pmax,Rle-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Extremes.Rd:64: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/IQR.Rd:44: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Ontology.Rd:26: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Ontology.Rd:29: missing file link 'Ontology,GOTerms-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/Ontology.Rd:31: missing file link 'GOTerms'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/annotation.Rd:34: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/annotation.Rd:37: missing file link 'annotation,eSet-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/annotation.Rd:39: missing file link 'eSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/append.Rd:54: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/append.Rd:57: missing file link 'append,Vector,Vector-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/append.Rd:59: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.data.frame.Rd:50: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.data.frame.Rd:53: missing file link 'as.data.frame,DataFrame-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.data.frame.Rd:55: missing file link 'as.data.frame,Ranges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.data.frame.Rd:57: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.data.frame.Rd:57: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:15: missing file link 'as.vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:30: missing file link 'as.vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:38: missing file link 'as.vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:47: missing file link 'as.vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:53: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:56: missing file link 'as.vector,Rle-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:57: missing file link 'as.vector,AtomicList-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:59: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/as.vector.Rd:60: missing file link 'AtomicList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/boxplot.Rd:44: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/boxplot.Rd:47: missing file link 'boxplot,FeatureSet-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/boxplot.Rd:49: missing file link 'FeatureSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/cbind.Rd:53: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/cbind.Rd:56: missing file link 'cbind,DataFrame-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/cbind.Rd:58: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/clusterApply.Rd:96: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:69: missing file link 'AnnotatedDataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:70: missing file link 'MIAME'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:71: missing file link 'eSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:84: missing file link 'combine,AnnotatedDataFrame,AnnotatedDataFrame-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:85: missing file link 'combine,AssayData,AssayData-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/combine.Rd:86: missing file link 'combine,MIAME,MIAME-method'
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  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/start.Rd:62: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/strand.Rd:73: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/strand.Rd:76: missing file link 'strand,GRanges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/strand.Rd:78: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/subset.Rd:46: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/subset.Rd:49: missing file link 'subset,DataTable-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/subset.Rd:51: missing file link 'DataTable'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/t.Rd:44: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/t.Rd:47: missing file link 't,Hits-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/t.Rd:49: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/table.Rd:46: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/table.Rd:49: missing file link 'table,Rle-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/table.Rd:51: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/tapply.Rd:64: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/tapply.Rd:67: missing file link 'tapply,Vector,ANY-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/tapply.Rd:69: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unique.Rd:57: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unique.Rd:60: missing file link 'unique,Rle-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unique.Rd:62: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unlist.Rd:51: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unlist.Rd:54: missing file link 'unlist,List-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unlist.Rd:56: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:14: missing file link 'unsplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:33: missing file link 'unsplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:39: missing file link 'unsplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:48: missing file link 'unsplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:54: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:57: missing file link 'unsplit,List-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/unsplit.Rd:59: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/updateObject.Rd:130: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/var.Rd:14: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/var.Rd:32: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/var.Rd:36: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/var.Rd:45: missing file link 'var'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/var.Rd:51: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/weights.Rd:47: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/weights.Rd:50: missing file link 'weights,PLMset-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/weights.Rd:52: missing file link 'PLMset'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/which.Rd:57: missing file link 'NumericList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/which.Rd:69: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/which.Rd:72: missing file link 'which.max,NumericList-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/which.Rd:75: missing file link 'NumericList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/xtabs.Rd:52: missing file link 'selectMethod'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/xtabs.Rd:55: missing file link 'xtabs,DataTable-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/xtabs.Rd:57: missing file link 'DataTable'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocGenerics.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'utils' 'graphics' 'stats' 'parallel'
A package should be listed in only one of these fields.
* 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' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'rep':
  'rep.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 7.61   0.00    7.61
plotMA      5.20   0.15    5.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
testPackage 12.75   0.03   12.78
plotMA       5.80   0.16    5.95
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

Installation output

BiocGenerics.Rcheck/00install.out


install for i386

* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'append' in package 'BiocGenerics'
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'do.call' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'grep' in package 'BiocGenerics'
Creating a new generic function for 'grepl' in package 'BiocGenerics'
Creating a new generic function for 'is.unsorted' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'lengths' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'rowSums' in package 'BiocGenerics'
Creating a new generic function for 'colSums' in package 'BiocGenerics'
Creating a new generic function for 'rowMeans' in package 'BiocGenerics'
Creating a new generic function for 'colMeans' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unsplit' in package 'BiocGenerics'
Creating a new generic function for 'var' in package 'BiocGenerics'
Creating a new generic function for 'sd' in package 'BiocGenerics'
Creating a new generic function for 'which' in package 'BiocGenerics'
Creating a new generic function for 'which.max' in package 'BiocGenerics'
Creating a new generic function for 'which.min' in package 'BiocGenerics'
Creating a new generic function for 'IQR' in package 'BiocGenerics'
Creating a new generic function for 'mad' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
  converting help for package 'BiocGenerics'
    finding HTML links ... done
    BiocGenerics-package                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:31: missing file link 'rbind'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:36: missing file link 'anyDuplicated'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:41: missing file link 'pmax'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:42: missing file link 'pmin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:43: missing file link 'pmax.int'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:44: missing file link 'pmin.int'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:47: missing file link 'Reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:48: missing file link 'Filter'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:49: missing file link 'Find'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:50: missing file link 'Map'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:51: missing file link 'Position'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:54: missing file link 'mget'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:57: missing file link 'grepl'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:62: missing file link 'sapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:71: missing file link 'ncol'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:72: missing file link 'NROW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:73: missing file link 'NCOL'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:81: missing file link 'rep.int'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:83: missing file link 'rownames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:84: missing file link 'rownames<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:85: missing file link 'colnames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:86: missing file link 'colnames<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:89: missing file link 'union'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:90: missing file link 'intersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:91: missing file link 'setdiff'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:96: missing file link 'start<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:97: missing file link 'end'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:98: missing file link 'end<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:99: missing file link 'width'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:100: missing file link 'width<-'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:138: missing file link 'clusterCall'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:140: missing file link 'clusterApplyLB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:141: missing file link 'clusterEvalQ'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:142: missing file link 'clusterExport'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpwvnQoR/R.INSTALLcd0578dfa5/BiocGenerics/man/BiocGenerics-package.Rd:143: missing file link 'clusterMap'
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    updateObject                            html  
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** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.24.0.zip
* DONE (BiocGenerics)
In R CMD INSTALL
In R CMD INSTALL

Tests output

BiocGenerics.Rcheck/tests_i386/run_unitTests.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.

> require("BiocGenerics") || stop("unable to load BiocGenerics package")
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

[1] TRUE
> BiocGenerics:::.test()


RUNIT TEST PROTOCOL -- Wed Apr 11 22:30:44 2018 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocGenerics RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.03    0.04    2.06

BiocGenerics.Rcheck/tests_x64/run_unitTests.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.

> require("BiocGenerics") || stop("unable to load BiocGenerics package")
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

[1] TRUE
> BiocGenerics:::.test()


RUNIT TEST PROTOCOL -- Wed Apr 11 22:30:46 2018 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocGenerics RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.31    0.07    2.37

Example timings

BiocGenerics.Rcheck/examples_i386/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes0.010.000.02
IQR000
Ontology1.640.061.70
annotation000
append000
as.data.frame000
as.vector000
boxplot000
cbind000
clusterApply0.020.000.02
combine0.140.000.14
dbconn0.060.000.06
density000
do.call000
duplicated000
eval000
evalq000
fileName1.810.062.03
funprog000
get000
grep000
image000
is.unsorted000
lapply000
lengths0.220.000.22
mad000
mapply000
match000
matrix-summary0.000.000.03
mean000
normalize0.040.000.03
nrow000
order000
organism_species0.230.000.23
paste000
plotMA5.200.155.69
plotPCA3.940.043.98
rank000
relist000
rep0.000.010.01
residuals000
row_colnames0.020.000.02
score0.080.020.09
sets000
sort000
start0.060.000.06
strand0.100.000.09
subset0.030.000.04
t0.010.000.01
table000
tapply000
testPackage7.610.007.61
unique000
unlist0.020.000.02
unsplit000
updateObject0.280.000.28
var000
weights000
which0.020.000.01
xtabs000

BiocGenerics.Rcheck/examples_x64/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes000
IQR000
Ontology2.040.062.09
annotation0.020.000.02
append0.010.000.01
as.data.frame000
as.vector000
boxplot000
cbind000
clusterApply0.010.000.01
combine0.190.000.19
dbconn0.060.000.06
density000
do.call000
duplicated0.020.000.02
eval000
evalq000
fileName2.840.113.09
funprog000
get000
grep000
image000
is.unsorted000
lapply000
lengths0.110.000.11
mad000
mapply000
match000
matrix-summary0.020.000.02
mean000
normalize0.020.000.01
nrow0.010.000.02
order000
organism_species0.190.060.25
paste000
plotMA5.800.165.95
plotPCA4.500.014.52
rank000
relist000
rep000
residuals000
row_colnames0.020.000.02
score0.070.020.09
sets0.020.000.02
sort000
start0.060.000.06
strand0.110.000.11
subset0.050.000.05
t000
table000
tapply000
testPackage12.75 0.0312.78
unique0.020.000.02
unlist000
unsplit000
updateObject0.280.000.28
var000
weights000
which000
xtabs0.010.000.01