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CHECK report for BiocGenerics on tokay2

This page was generated on 2018-10-17 08:35:56 -0400 (Wed, 17 Oct 2018).

Package 128/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.26.0
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BiocGenerics
Branch: RELEASE_3_7
Last Commit: 5b2a6df
Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocGenerics
Version: 0.26.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocGenerics_0.26.0.tar.gz
StartedAt: 2018-10-17 00:44:01 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:45:28 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 86.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BiocGenerics_0.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.26.0'
* 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-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:31: file link 'rbind' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:36: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:41: file link 'pmax' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:42: file link 'pmin' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:43: file link 'pmax.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:44: file link 'pmin.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:47: file link 'Reduce' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:48: file link 'Filter' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:49: file link 'Find' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:50: file link 'Map' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:51: file link 'Position' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:54: file link 'mget' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:57: file link 'grepl' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:62: file link 'sapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:71: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:72: file link 'NROW' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:73: file link 'NCOL' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:81: file link 'rep.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:83: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:84: file link 'rownames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:85: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:86: file link 'colnames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:89: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:90: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:91: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:96: file link 'start<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:97: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:98: file link 'end<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:99: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:100: file link 'width<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:101: file link 'pos' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:139: file link 'clusterCall' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:141: file link 'clusterApplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:142: file link 'clusterEvalQ' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:143: file link 'clusterExport' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:144: file link 'clusterMap' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:145: file link 'clusterSplit' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:146: file link 'parLapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:147: file link 'parSapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:148: file link 'parApply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:149: file link 'parRapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:150: file link 'parCapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:151: file link 'parLapplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:152: file link 'parSapplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:159: file link 'annotation<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:164: file link 'dbfile' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:172: file link 'organism' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:173: file link 'organism<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:174: file link 'species' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:175: file link 'species<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:178: file link 'path<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:179: file link 'basename' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:180: file link 'basename<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:181: file link 'dirname' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:182: file link 'dirname<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:189: file link 'score<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:192: file link 'strand<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:193: file link 'invertStrand' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:232: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:18: file link 'pmax' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:38: file link 'pmax' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:44: file link 'pmax' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:53: file link 'pmax' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:59: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:62: file link 'pmax,Rle-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Extremes.Rd:64: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/IQR.Rd:44: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Ontology.Rd:26: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Ontology.Rd:29: file link 'Ontology,GOTerms-method' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/Ontology.Rd:31: file link 'GOTerms' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/annotation.Rd:34: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/annotation.Rd:37: file link 'annotation,eSet-method' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/annotation.Rd:39: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/append.Rd:54: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/append.Rd:57: file link 'append,Vector,Vector-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/append.Rd:59: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/as.data.frame.Rd:50: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/as.data.frame.Rd:53: file link 'as.data.frame,DataFrame-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/as.data.frame.Rd:55: missing file link 'as.data.frame,IntegerRanges-method'
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/density.Rd:45: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/duplicated.Rd:72: file link 'duplicated,Rle-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/duplicated.Rd:74: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/eval.Rd:58: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/evalq.Rd:12: file link 'evalq' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/evalq.Rd:34: file link 'evalq' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/evalq.Rd:40: file link 'evalq' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/evalq.Rd:45: file link 'evalq' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/fileName.Rd:29: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/funprog.Rd:55: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/funprog.Rd:64: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/image.Rd:51: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/is.unsorted.Rd:63: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/lapply.Rd:61: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/lengths.Rd:45: file link 'elementNROWS' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/lengths.Rd:64: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/lengths.Rd:67: file link 'lengths,Vector-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/lengths.Rd:69: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/mad.Rd:46: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/mapply.Rd:9: file link 'sapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/match.Rd:61: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/match.Rd:64: file link 'match,Hits,Hits-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/match.Rd:66: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/matrix-summary.Rd:53: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/mean.Rd:46: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/mean.Rd:49: file link 'mean,Rle-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/mean.Rd:51: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/normalize.Rd:38: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/normalize.Rd:41: file link 'normalize,AffyBatch-method' in package 'affy' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/normalize.Rd:42: file link 'normalize,FeatureSet-method' in package 'oligo' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/normalize.Rd:44: file link 'AffyBatch' in package 'affy' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/normalize.Rd:44: file link 'FeatureSet' in package 'oligoClasses' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/nrow.Rd:50: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/nrow.Rd:53: file link 'nrow,DataFrame-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/nrow.Rd:55: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/order.Rd:73: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/order.Rd:76: missing file link 'order,IntegerRanges-method'
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/updateObject.Rd:130: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:47: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:50: file link 'weights,PLMset-method' in package 'affyPLM' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:52: file link 'PLMset' in package 'affyPLM' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:57: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:69: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:72: file link 'which.max,NumericList-method' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:75: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:52: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:55: file link 'xtabs,DataTable-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:57: file link 'DataTable' in package 'S4Vectors' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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 ... WARNING
Missing link or links in documentation object 'as.data.frame.Rd':
  '[IRanges]{as.data.frame,IntegerRanges-method}'

Missing link or links in documentation object 'order.Rd':
  '[IRanges]{order,IntegerRanges-method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'clusterApply':
parLapply
  Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, fun, ...)
  Argument names in code not in docs:
    chunk.size
parSapply
  Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE, chunk.size = NULL)
  Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE)
  Argument names in code not in docs:
    chunk.size
parApply
  Code: function(cl = NULL, X, MARGIN, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, MARGIN, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parRapply
  Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, x, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parCapply
  Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, x, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parLapplyLB
  Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, fun, ...)
  Argument names in code not in docs:
    chunk.size
parSapplyLB
  Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE, chunk.size = NULL)
  Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE)
  Argument names in code not in docs:
    chunk.size

* 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
plotMA 5.58   0.64    6.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
plotMA 8.01   0.36    8.39
* 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: 3 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

Installation output

BiocGenerics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BiocGenerics_0.26.0.tar.gz && rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocGenerics.buildbin-libdir BiocGenerics_0.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BiocGenerics_0.26.0.zip && rm BiocGenerics_0.26.0.tar.gz BiocGenerics_0.26.0.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 46765  100 46765    0     0   688k      0 --:--:-- --:--:-- --:--:--  774k

install for i386

* installing *source* package 'BiocGenerics' ...
** R
** inst
** byte-compile and prepare 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'
Creating a new generic function for 'basename' in package 'BiocGenerics'
Creating a new generic function for 'dirname' 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-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:31: file link 'rbind' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:36: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:41: file link 'pmax' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:42: file link 'pmin' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:43: file link 'pmax.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:44: file link 'pmin.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:47: file link 'Reduce' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:48: file link 'Filter' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:49: file link 'Find' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:50: file link 'Map' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:51: file link 'Position' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:54: file link 'mget' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:57: file link 'grepl' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:62: file link 'sapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:71: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:72: file link 'NROW' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:73: file link 'NCOL' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:81: file link 'rep.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:83: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:84: file link 'rownames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:85: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:86: file link 'colnames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:89: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:90: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:91: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:96: file link 'start<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:97: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:98: file link 'end<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:99: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:100: file link 'width<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:101: file link 'pos' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:139: file link 'clusterCall' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:141: file link 'clusterApplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:142: file link 'clusterEvalQ' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:143: file link 'clusterExport' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:144: file link 'clusterMap' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:145: file link 'clusterSplit' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:146: file link 'parLapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:147: file link 'parSapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:148: file link 'parApply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:149: file link 'parRapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/BiocGenerics-package.Rd:150: file link 'parCapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/start.Rd:71: file link 'pos,IPos-method' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/start.Rd:73: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
    strand                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/strand.Rd:73: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/strand.Rd:76: file link 'strand,GRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/strand.Rd:78: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    subset                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/subset.Rd:46: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/subset.Rd:49: file link 'subset,DataTable-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/subset.Rd:51: file link 'DataTable' in package 'S4Vectors' does not exist and so has been treated as a topic
    t                                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/t.Rd:44: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/t.Rd:47: file link 't,Hits-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/t.Rd:49: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    table                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/table.Rd:46: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/table.Rd:49: file link 'table,Rle-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/table.Rd:51: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    tapply                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/tapply.Rd:64: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/tapply.Rd:67: file link 'tapply,Vector,ANY-method' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/tapply.Rd:69: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
    testPackage                             html  
    unique                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unique.Rd:57: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unique.Rd:60: file link 'unique,Rle-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unique.Rd:62: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    unlist                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unlist.Rd:51: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unlist.Rd:54: file link 'unlist,List-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unlist.Rd:56: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    unsplit                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:14: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:33: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:39: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:48: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:54: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:57: file link 'unsplit,List-method' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/unsplit.Rd:59: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    updateObject                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/updateObject.Rd:130: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
    var                                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/var.Rd:14: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/var.Rd:32: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/var.Rd:36: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/var.Rd:45: file link 'var' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/var.Rd:51: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
    weights                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:47: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:50: file link 'weights,PLMset-method' in package 'affyPLM' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/weights.Rd:52: file link 'PLMset' in package 'affyPLM' does not exist and so has been treated as a topic
    which                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:57: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:69: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:72: file link 'which.max,NumericList-method' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/which.Rd:75: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
    xtabs                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:52: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:55: file link 'xtabs,DataTable-method' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpg1xhre/R.INSTALL1150e8b3dcd/BiocGenerics/man/xtabs.Rd:57: file link 'DataTable' in package 'S4Vectors' does not exist and so has been treated as a topic
** 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_0.26.0.zip
* DONE (BiocGenerics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BiocGenerics' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

BiocGenerics.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 Oct 17 00:45:15 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 
   1.23    0.04    1.26

BiocGenerics.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 Oct 17 00:45:17 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 
   1.10    0.06    1.15

Example timings

BiocGenerics.Rcheck/examples_i386/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes0.010.000.01
IQR000
Ontology2.840.173.01
annotation0.030.000.04
append000
as.data.frame000
as.vector0.020.000.01
boxplot000
cbind000
clusterApply0.030.000.03
combine0.070.000.08
dbconn0.080.000.07
density000
do.call000
duplicated0.010.000.02
eval000
evalq000
fileName2.750.102.98
funprog0.020.000.02
get000
grep000
image000
is.unsorted000
lapply000
lengths0.040.010.06
mad000
mapply0.020.000.02
match000
matrix-summary000
mean000
normalize0.030.000.03
nrow0.020.000.01
order000
organism_species0.390.000.39
paste000
path0.010.020.03
plotMA5.580.646.22
plotPCA2.590.052.64
rank000
relist000
rep000
residuals000
row_colnames000
score0.050.030.08
sets000
sort0.010.000.02
start0.050.000.05
strand0.080.000.07
subset0.010.000.02
t0.020.000.01
table000
tapply000
testPackage0.420.000.55
unique000
unlist0.020.000.02
unsplit000
updateObject0.230.090.33
var0.020.000.01
weights000
which0.010.000.02
xtabs000

BiocGenerics.Rcheck/examples_x64/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes0.010.000.01
IQR000
Ontology2.570.102.67
annotation0.000.020.01
append000
as.data.frame000
as.vector000
boxplot000
cbind000
clusterApply0.020.010.03
combine0.060.000.06
dbconn0.050.000.05
density0.000.020.01
do.call000
duplicated000
eval000
evalq000
fileName2.810.163.11
funprog000
get0.020.000.02
grep000
image000
is.unsorted0.010.000.01
lapply000
lengths0.080.000.08
mad000
mapply000
match0.020.000.01
matrix-summary000
mean000
normalize0.040.000.03
nrow0.010.000.02
order000
organism_species0.380.040.42
paste0.010.000.01
path0.050.000.05
plotMA8.010.368.39
plotPCA3.410.033.44
rank000
relist0.010.000.01
rep000
residuals000
row_colnames0.020.000.02
score0.110.020.12
sets0.010.000.02
sort000
start0.060.000.06
strand0.080.000.08
subset0.030.000.03
t000
table0.020.000.02
tapply000
testPackage0.320.000.33
unique0.020.000.01
unlist000
unsplit000
updateObject0.300.010.32
var000
weights0.010.000.01
which000
xtabs000