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CHECK report for BiocGenerics on tokay1

This page was generated on 2020-08-12 11:39:50 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocGenerics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 152/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.35.4
Bioconductor Package Maintainer
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/BiocGenerics
Branch: master
Last Commit: 59d6941
Last Changed Date: 2020-06-04 12:59:02 -0400 (Thu, 04 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocGenerics
Version: 0.35.4
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocGenerics_0.35.4.tar.gz
StartedAt: 2020-08-12 00:44:03 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:45:42 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BiocGenerics_0.35.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocGenerics.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '0.35.4'
* 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:32: file link 'rbind' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:36: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:37: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:38: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:43: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:48: file link 'pmax' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:49: file link 'pmin' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:50: file link 'pmax.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:51: file link 'pmin.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:54: file link 'Reduce' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:55: file link 'Filter' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:56: file link 'Find' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:57: file link 'Map' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:58: file link 'Position' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:61: file link 'mget' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:64: file link 'grepl' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:69: file link 'sapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:74: file link '%in%' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:77: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:78: file link 'NROW' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:79: file link 'NCOL' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:87: file link 'rep.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:89: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:90: file link 'rownames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:91: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:92: file link 'colnames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:95: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:96: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:97: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:102: file link 'start<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:103: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:104: file link 'end<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:105: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:106: file link 'width<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:107: file link 'pos' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:124: file link 'which.max' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:152: file link 'clusterCall' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:154: file link 'clusterApplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:155: file link 'clusterEvalQ' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:156: file link 'clusterExport' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:157: file link 'clusterMap' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:158: file link 'clusterSplit' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:159: file link 'parLapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:160: file link 'parSapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:161: file link 'parApply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:162: file link 'parRapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:163: file link 'parCapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:164: file link 'parLapplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:165: file link 'parSapplyLB' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:172: file link 'annotation<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:177: file link 'dbfile' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:187: file link 'organism' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:188: file link 'organism<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:189: file link 'species' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:190: file link 'species<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:193: file link 'path<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:194: file link 'basename' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:195: file link 'basename<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:196: file link 'dirname' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:197: file link 'dirname<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:204: file link 'score<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:207: file link 'strand<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:208: file link 'invertStrand' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:213: file link 'type<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:252: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/append.Rd:54: 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/get.Rd:64: 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/match.Rd:66: 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/match.Rd:70: file link '%in%,Rle,ANY-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/match.Rd:72: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/match.Rd:73: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/mean.Rd:46: 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/unlist.Rd:56: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/unsplit.Rd:59: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/updateObject.Rd:130: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/var.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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.Rd:49: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.Rd:52: file link 'which,DelayedArray-method' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.Rd:54: file link 'DelayedArray' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.min.Rd:50: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.min.Rd:62: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.min.Rd:65: 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.min.Rd:67: file link 'NumericList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/xtabs.Rd:55: file link 'xtabs,DataFrame-method' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/xtabs.Rd:57: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-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 ... 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 (user + system) or elapsed time > 5s
       user system elapsed
plotMA  8.7   1.11   10.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
plotMA 9.23   0.28    9.52
* 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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.



Installation output

BiocGenerics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BiocGenerics_0.35.4.tar.gz && rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocGenerics.buildbin-libdir BiocGenerics_0.35.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BiocGenerics_0.35.4.zip && rm BiocGenerics_0.35.4.tar.gz BiocGenerics_0.35.4.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 49091  100 49091    0     0  1073k      0 --:--:-- --:--:-- --:--:-- 1169k

install for i386

* installing *source* package 'BiocGenerics' ...
** using staged installation
** 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 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' 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.min' in package 'BiocGenerics'
Creating a new generic function for 'which.max' 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-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:32: file link 'rbind' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:36: file link 'rowSums' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:37: file link 'colMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:38: file link 'rowMeans' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:43: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:48: file link 'pmax' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:49: file link 'pmin' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:50: file link 'pmax.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:51: file link 'pmin.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:54: file link 'Reduce' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:55: file link 'Filter' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:56: file link 'Find' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:57: file link 'Map' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:58: file link 'Position' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:61: file link 'mget' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:64: file link 'grepl' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:69: file link 'sapply' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:74: file link '%in%' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:77: file link 'ncol' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:78: file link 'NROW' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:79: file link 'NCOL' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:87: file link 'rep.int' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:89: file link 'rownames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:90: file link 'rownames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:91: file link 'colnames' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:92: file link 'colnames<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:95: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:96: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:97: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:102: file link 'start<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:103: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:104: file link 'end<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:105: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:106: file link 'width<-' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/BiocGenerics-package.Rd:107: file link 'pos' in package 'BiocGenerics' does not exist and so has been treated as a topic
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    score                                   html  
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    sets                                    html  
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    sort                                    html  
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    start                                   html  
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    strand                                  html  
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    subset                                  html  
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    t                                       html  
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    table                                   html  
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    tapply                                  html  
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    testPackage                             html  
    toTable                                 html  
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    type                                    html  
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    unique                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/unique.Rd:57: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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    unlist                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/unlist.Rd:51: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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    unsplit                                 html  
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    updateObject                            html  
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    var                                     html  
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    weights                                 html  
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    which                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSEFlA2/R.INSTALL117439ad15de/BiocGenerics/man/which.Rd:49: file link 'selectMethod' in package 'methods' does not exist and so has been treated as a topic
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    which.min                               html  
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    xtabs                                   html  
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** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.35.4.zip
* DONE (BiocGenerics)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BiocGenerics' successfully unpacked and MD5 sums checked

Tests output

BiocGenerics.Rcheck/tests_i386/run_unitTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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


RUNIT TEST PROTOCOL -- Wed Aug 12 00:45:31 2020 
*********************************************** 
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 
   0.89    0.10    0.96 

BiocGenerics.Rcheck/tests_x64/run_unitTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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


RUNIT TEST PROTOCOL -- Wed Aug 12 00:45:32 2020 
*********************************************** 
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 
   1.15    0.07    1.21 

Example timings

BiocGenerics.Rcheck/examples_i386/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package0.010.000.02
Extremes0.000.020.01
IQR000
Ontology2.550.172.72
annotation0.020.000.02
append000
as.data.frame000
as.list0.030.000.03
as.vector000
boxplot0.110.030.14
cbind0.010.000.02
clusterApply0.020.000.02
colSums000
combine0.040.000.05
dbconn0.170.000.17
density000
dims000
do.call000
duplicated000
eval000
evalq000
fileName2.860.213.08
funprog000
get0.020.000.02
grep000
image0.040.000.04
is.unsorted000
lapply000
mad0.020.000.02
mapply000
match000
mean0.010.000.02
normalize0.050.000.04
nrow0.020.000.02
order000
organism_species0.450.000.45
paste000
path0.050.000.05
plotMA 8.70 1.1110.34
plotPCA2.550.112.66
rank0.010.000.01
relist000
rep000
residuals000
row_colnames0.020.000.02
score0.080.000.08
sets000
sort000
start0.040.010.06
strand0.050.030.08
subset0.010.020.03
t0.020.000.02
table000
tapply000
testPackage0.330.000.32
toTable0.060.000.07
type0.540.030.58
unique000
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var0.020.000.01
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which0.070.020.10
which.min0.050.000.05
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BiocGenerics.Rcheck/examples_x64/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
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IQR000
Ontology2.220.142.36
annotation0.000.010.02
append000
as.data.frame000
as.list0.020.000.01
as.vector000
boxplot0.140.000.14
cbind0.010.020.03
clusterApply0.020.000.01
colSums000
combine0.050.000.05
dbconn0.120.010.14
density000
dims0.020.000.01
do.call000
duplicated000
eval000
evalq000
fileName2.660.132.78
funprog0.010.000.02
get000
grep000
image0.070.000.06
is.unsorted000
lapply000
mad0.010.000.01
mapply000
match000
mean0.020.000.02
normalize0.050.000.05
nrow0.010.000.01
order000
organism_species0.300.030.33
paste000
path0.030.000.03
plotMA9.230.289.52
plotPCA2.860.032.89
rank0.030.000.03
relist000
rep000
residuals000
row_colnames0.020.000.02
score0.100.000.11
sets0.000.020.02
sort0.020.000.01
start0.090.000.09
strand0.140.000.15
subset0.050.000.04
t000
table0.020.000.02
tapply000
testPackage0.530.000.53
toTable0.110.010.12
type1.790.051.85
unique000
unlist000
unsplit0.000.010.02
updateObject0.220.000.22
var000
weights000
which0.100.020.11
which.min0.080.000.08
xtabs0.060.000.06