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CHECK report for S4Vectors on tokay1

This page was generated on 2019-04-13 11:23:53 -0400 (Sat, 13 Apr 2019).

Package 1376/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
S4Vectors 0.20.1
Bioconductor Package Maintainer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/S4Vectors
Branch: RELEASE_3_8
Last Commit: 1878b29
Last Changed Date: 2018-11-08 19:08:23 -0400 (Thu, 08 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: S4Vectors
Version: 0.20.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings S4Vectors_0.20.1.tar.gz
StartedAt: 2019-04-13 05:17:30 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:20:38 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 187.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: S4Vectors.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings S4Vectors_0.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'S4Vectors/DESCRIPTION' ... OK
* this is package 'S4Vectors' version '0.20.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'S4Vectors' can be installed ... WARNING
Found the following significant warnings:
  LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/DataTable-class.Rd:56: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:80: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:176: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:187: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:282: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:285: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:101: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:103: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:59: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:74: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:75: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:83: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:84: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:85: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:95: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:144: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:152: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:205: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:206: file link 'LogicalList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:206: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:207: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:258: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:262: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:94: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:105: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:115: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:127: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:156: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:189: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:192: file link 'within' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:207: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:210: file link 'within' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:214: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:46: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:47: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:105: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:202: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:221: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:363: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-runstat.Rd:95: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:85: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:89: file link 'SimpleIntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:215: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:223: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:358: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:373: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:374: file link 'XRaw' in package 'XVector' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:292: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:325: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:341: missing file link 'IntegerRanges-comparison'
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:90: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:91: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:92: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:38: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:38: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:42: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:44: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:45: file link 'SimpleAtomicList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:96: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:97: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/integer-utils.Rd:70: file link 'seq_len' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:44: file link 'window' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:45: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:47: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:64: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* 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
Unexported objects imported by ':::' calls:
  'data.table:::as.data.frame.data.table'
  'stats:::na.exclude.data.frame' 'stats:::na.omit.data.frame'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalSeparately,FilterRules : <anonymous>: no visible global function
  definition for '.'
Undefined global functions or variables:
  .
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Vector-comparison.Rd':
  '[IRanges]{IntegerRanges-comparison}'

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'cbind.DataFrame' 'head.LLint' 'pcompareRecursively' 'phead' 'ptail'
  'rbind.DataFrame' 'selectHits' 't.Hits' 't.HitsList' 'tail.LLint'
  'window.LLint'
Undocumented S4 classes:
  'integer_OR_LLint' 'list_OR_List'
Undocumented S4 methods:
  generic '!' and siglist 'List'
  generic '<=' and siglist 'List,List'
  generic '<=' and siglist 'List,list'
  generic '<=' and siglist 'list,List'
  generic '==' and siglist 'List,List'
  generic '==' and siglist 'List,list'
  generic '==' and siglist 'list,List'
  generic 'NSBS' and siglist 'Rle'
  generic '[' and siglist 'LLint'
  generic 'anyDuplicated' and siglist 'Rle'
  generic 'anyDuplicated' and siglist 'RleNSBS'
  generic 'anyNA' and siglist 'List'
  generic 'anyNA' and siglist 'Rle'
  generic 'as.integer' and siglist 'RleNSBS'
  generic 'by' and siglist 'Vector'
  generic 'coerce' and siglist 'ANY,DataTable_OR_NULL'
  generic 'countMatches' and siglist 'ANY'
  generic 'do.call' and siglist 'ANY,List'
  generic 'droplevels' and siglist 'DataFrame'
  generic 'duplicated' and siglist 'List'
  generic 'eval' and siglist 'expression,Vector'
  generic 'eval' and siglist 'language,Vector'
  generic 'extractROWS' and siglist 'DataFrame,ANY'
  generic 'extractROWS' and siglist 'LLint,ANY'
  generic 'extractROWS' and siglist 'LLint,NSBS'
  generic 'extractROWS' and siglist 'LLint,RangeNSBS'
  generic 'extractROWS' and siglist 'Rle,NSBS'
  generic 'extractROWS' and siglist 'Rle,RleNSBS'
  generic 'extractROWS' and siglist 'Vector,ANY'
  generic 'filterRules' and siglist 'FilterResults'
  generic 'from' and siglist 'HitsList'
  generic 'getListElement' and siglist 'SimpleList'
  generic 'grep' and siglist 'ANY,Rle'
  generic 'grepl' and siglist 'ANY,Rle'
  generic 'head' and siglist 'LLint'
  generic 'is.na' and siglist 'List'
  generic 'is.unsorted' and siglist 'List'
  generic 'isStrictlySorted' and siglist 'Rle'
  generic 'isStrictlySorted' and siglist 'RleNSBS'
  generic 'length' and siglist 'RleNSBS'
  generic 'match' and siglist 'ANY,Rle'
  generic 'match' and siglist 'List,List'
  generic 'match' and siglist 'List,Vector'
  generic 'match' and siglist 'List,list'
  generic 'match' and siglist 'List,vector'
  generic 'match' and siglist 'Rle,Rle'
  generic 'match' and siglist 'list,List'
  generic 'order' and siglist 'List'
  generic 'order' and siglist 'Rle'
  generic 'pcompare' and siglist 'List,List'
  generic 'pcompare' and siglist 'List,list'
  generic 'pcompare' and siglist 'list,List'
  generic 'pcompareRecursively' and siglist 'List'
  generic 'pcompareRecursively' and siglist 'list'
  generic 'rank' and siglist 'List'
  generic 'rank' and siglist 'Rle'
  generic 'rep.int' and siglist 'LLint'
  generic 'rep' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'ANY'
  generic 'replaceROWS' and siglist 'DataFrame'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'replaceROWS' and siglist 'Vector'
  generic 'sort' and siglist 'DataTable'
  generic 'sort' and siglist 'List'
  generic 'sort' and siglist 'SortedByQueryHits'
  generic 'summary' and siglist 'FilterResults'
  generic 't' and siglist 'Pairs'
  generic 'tail' and siglist 'LLint'
  generic 'to' and siglist 'HitsList'
  generic 'transform' and siglist 'Vector'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'updateObject' and siglist 'Vector'
  generic 'window' and siglist 'LLint'
  generic 'with' and siglist 'Vector'
  generic 'xtabs' and siglist 'Vector'
  generic 'xtfrm' and siglist 'Rle'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/libs/i386/S4Vectors.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
shiftApply-methods 14.98   2.12   17.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
shiftApply-methods 14.28   2.26   16.54
* 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 for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck/00check.log'
for details.



Installation output

S4Vectors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/S4Vectors_0.20.1.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.20.1.zip && rm S4Vectors_0.20.1.tar.gz S4Vectors_0.20.1.zip
###
##############################################################################
##############################################################################


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100  224k  100  224k    0     0  5890k      0 --:--:-- --:--:-- --:--:-- 6411k

install for i386

* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_increase_buflength':
AEbufs.c:31:2: warning: large integer implicitly truncated to unsigned type [-Woverflow]
  return MAX_BUFLENGTH;
  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function 'Hits_new':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1348:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define defineVar  Rf_defineVar
                    ^
Hits_class.c:216:12: note: 'revmap' was declared here
  SEXP ans, revmap, symbol;
            ^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (nodup0 && is_used->elts[ans_elt - 1])
                        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   if (sprintf(val_buf, "%lld", from_elt) < 0)
   ^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'check_integer_runs':
Rle_class.c:218:20: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *max_len_out_p = len_out;
                    ^
Rle_class.c: In function '_construct_character_Rle':
Rle_class.c:509:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     len_out += len_in;
             ^
Rle_class.c:489:30: note: 'len_out' was declared here
  unsigned long long int sum, len_out;
                              ^
Rle_class.c: In function '_construct_raw_Rle':
Rle_class.c:606:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
     len_out += len_in;
             ^
Rle_class.c:587:30: note: 'len_out' was declared here
  unsigned long long int sum, len_out;
                              ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function]
 static void sort_uchar_array(unsigned char *x, int nelt, int desc)
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'complete.cases' from package 'stats' in package 'S4Vectors'
Creating a new generic function for 'expand.grid' in package 'S4Vectors'
Creating a generic function for '%in%' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'findMatches' in package 'S4Vectors'
Creating a generic function for 'setequal' from package 'base' in package 'S4Vectors'
Creating a generic function for 'as.factor' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tabulate' from package 'base' in package 'S4Vectors'
Creating a generic function for 'cov' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'cor' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'runmed' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substring' from package 'base' in package 'S4Vectors'
Creating a generic function for 'chartr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tolower' from package 'base' in package 'S4Vectors'
Creating a generic function for 'toupper' from package 'base' in package 'S4Vectors'
Creating a generic function for 'sub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'gsub' from package 'base' in package 'S4Vectors'
in method for 'coerce' with signature '"data.table","DataFrame"': no definition for class "data.table"
** help
*** installing help indices
  converting help for package 'S4Vectors'
    finding HTML links ... done
    Annotated-class                         html  
    DataFrame-class                         html  
    DataTable-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/DataTable-class.Rd:56: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
    FilterMatrix-class                      html  
    FilterRules-class                       html  
    Hits-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:80: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:176: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:187: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:282: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:285: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
    Hits-comparison                         html  
    Hits-setops                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
    HitsList-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
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    LLint-class                             html  
    List-class                              html  
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    List-utils                              html  
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    Pairs-class                             html  
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    Rle-class                               html  
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    Rle-runstat                             html  
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    Rle-utils                               html  
    S4Vectors-internals                     html  
    SimpleList-class                        html  
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    Vector-class                            html  
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    Vector-merge                            html  
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    Vector-setops                           html  
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    aggregate-methods                       html  
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    expand-methods                          html  
    integer-utils                           html  
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    shiftApply-methods                      html  
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    subsetting-utils                        html  
    zip-methods                             html  
** building package indices
** installing vignettes
   'RleTricks.Rnw' using 'UTF-8' 
   'S4QuickOverview.Rnw' using 'UTF-8' 
   'S4VectorsOverview.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function 'Hits_new':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1348:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define defineVar  Rf_defineVar
                    ^
Hits_class.c:216:12: note: 'revmap' was declared here
  SEXP ans, revmap, symbol;
            ^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (nodup0 && is_used->elts[ans_elt - 1])
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   if (sprintf(val_buf, "%lld", from_elt) < 0)
   ^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
LLint_class.c: In function 'llints_summary':
LLint_class.c:791:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res = _safe_llint_mult(res, in_elt);
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function]
 static void sort_uchar_array(unsigned char *x, int nelt, int desc)
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.20.1.zip
* DONE (S4Vectors)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

S4Vectors.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

[1] TRUE
> S4Vectors:::.test()

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb


RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:23 2019 
*********************************************** 
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 60 test functions, 0 errors, 0 failures
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   7.37    0.18    8.28 

S4Vectors.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

[1] TRUE
> S4Vectors:::.test()

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb


RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:31 2019 
*********************************************** 
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 60 test functions, 0 errors, 0 failures
Number of test functions: 60 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   7.65    0.17    7.81 

Example timings

S4Vectors.Rcheck/examples_i386/S4Vectors-Ex.timings

nameusersystemelapsed
Annotated-class0.720.000.72
DataFrame-class0.200.020.22
DataTable-class0.020.000.02
FilterRules-class0.090.000.09
Hits-class0.060.000.07
Hits-comparison0.030.000.03
Hits-setops0.070.000.06
LLint-class0.030.000.03
List-class000
List-utils0.090.000.10
Pairs-class0.050.000.04
Rle-class0.060.000.06
Rle-runstat0.130.000.13
Rle-utils0.010.000.02
SimpleList-class0.020.020.03
Vector-class000
Vector-comparison0.030.000.03
Vector-merge1.290.151.45
Vector-setops000
aggregate-methods0.100.030.13
character-utils0.010.000.01
expand-methods0.160.020.17
integer-utils000
isSorted000
shiftApply-methods14.98 2.1217.11
split-methods0.060.000.06
zip-methods000

S4Vectors.Rcheck/examples_x64/S4Vectors-Ex.timings

nameusersystemelapsed
Annotated-class0.770.000.76
DataFrame-class0.220.030.25
DataTable-class0.030.000.03
FilterRules-class0.100.000.09
Hits-class0.080.000.08
Hits-comparison0.030.000.03
Hits-setops0.060.000.06
LLint-class0.030.000.03
List-class000
List-utils0.110.000.11
Pairs-class0.050.000.05
Rle-class0.060.000.06
Rle-runstat0.140.000.14
Rle-utils0.030.000.04
SimpleList-class0.030.000.03
Vector-class000
Vector-comparison0.050.000.04
Vector-merge1.480.071.55
Vector-setops000
aggregate-methods0.100.000.09
character-utils000
expand-methods0.190.000.19
integer-utils0.010.000.02
isSorted000
shiftApply-methods14.28 2.2616.54
split-methods0.050.000.05
zip-methods0.020.000.02