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CHECK report for GenomicRanges on tokay1

This page was generated on 2020-04-15 12:19:10 -0400 (Wed, 15 Apr 2020).

Package 685/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenomicRanges
Branch: RELEASE_3_10
Last Commit: b816804
Last Changed Date: 2020-01-30 16:16:34 -0400 (Thu, 30 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 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: GenomicRanges
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenomicRanges_1.38.0.tar.gz
StartedAt: 2020-04-15 03:27:17 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:34:45 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 448.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicRanges.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GenomicRanges_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.38.0'
* package encoding: UTF-8
* 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 'GenomicRanges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:46: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:47: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:48: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:49: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:55: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:73: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:74: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:74: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:77: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:92: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:94: file link 'UnstitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:95: file link 'StitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:112: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:132: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:133: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:134: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:136: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:148: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:150: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:151: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:152: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:202: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:225: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:254: file link 'snpsBySeqname' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:255: file link 'snpsByOverlaps' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:256: file link 'snpsById' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:257: file link 'SNPlocs' in package 'BSgenome' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:260: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:100: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:102: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:104: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:106: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:124: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:128: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:183: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:189: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:289: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:313: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:356: file link 'ManyToOneGrouping' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:371: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:408: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:436: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:472: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:473: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:476: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:476: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:485: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:493: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:530: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:530: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:531: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:28: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:31: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:32: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:41: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:66: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:69: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:78: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:88: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:93: file link 'unfactor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:98: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:107: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:114: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:118: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:127: file link 'Factor' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesFactor-class.Rd:130: file link 'anyDuplicated' in package 'BiocGenerics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesList-class.Rd:194: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesList-class.Rd:347: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesList-class.Rd:350: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRangesList-class.Rd:353: file link 'DataFrameList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRanges-comparison.Rd:115: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRangesList-class.Rd:91: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRangesList-class.Rd:92: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GenomicRangesList-class.Rd:92: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/absoluteRanges.Rd:39: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/absoluteRanges.Rd:41: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/absoluteRanges.Rd:50: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/absoluteRanges.Rd:65: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/absoluteRanges.Rd:86: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:13: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:16: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:17: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:19: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:20: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:46: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:58: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:62: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.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-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:81: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/coverage-methods.Rd:86: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:25: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:26: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:27: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:29: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:30: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:31: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:103: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/findOverlaps-methods.Rd:117: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:16: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:17: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:19: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:21: file link 'rglist' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:32: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:40: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:46: file link 'ranges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:49: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:50: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:79: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:82: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:83: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomic-range-squeezers.Rd:84: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:20: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:49: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:60: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:80: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:91: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/genomicvars.Rd:105: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/inter-range-methods.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/inter-range-methods.Rd:103: file link 'gaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/inter-range-methods.Rd:112: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/inter-range-methods.Rd:136: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/inter-range-methods.Rd:144: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:39: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:40: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:83: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:87: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:91: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:160: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:122: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:144: file link 'getTable' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:148: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:69: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:142: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:145: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:158: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:159: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:45: file link 'punion' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:45: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:46: file link 'psetdiff' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:46: file link 'pgap' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:47: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:155: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:156: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:167: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:52: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.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-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:65: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.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-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:96: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:12: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:12: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:30: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:35: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:65: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tileGenome.Rd:68: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tileGenome.Rd:70: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.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 ... OK
* 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 'GenomicRangesList-class.Rd':
  '[IRanges]{RangesList}'

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'sort.GRangesList'
Undocumented S4 methods:
  generic 'sort' and siglist 'CompressedGRangesList'
  generic 'update' and siglist 'DelegatingGenomicRanges'
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 ... WARNING
Documented arguments not in \usage in documentation object 'intra-range-methods':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.10-bioc/R/library/GenomicRanges/libs/i386/GenomicRanges.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/GenomicRanges/libs/x64/GenomicRanges.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
genomicvars              44.75  11.36   56.11
GPos-class               37.92   4.61   43.56
makeGRangesFromDataFrame  0.44   0.03   10.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
genomicvars              45.91  12.23   58.14
GPos-class               34.76   4.48   39.33
makeGRangesFromDataFrame  0.50   0.00   11.72
* 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: 4 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.

Installation output

GenomicRanges.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz && rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicRanges.buildbin-libdir GenomicRanges_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.38.0.zip && rm GenomicRanges_1.38.0.tar.gz GenomicRanges_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  155k  100  155k    0     0  3659k      0 --:--:-- --:--:-- --:--:-- 3987k

install for i386

* installing *source* package 'GenomicRanges' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.buildbin-libdir/00LOCK-GenomicRanges/00new/GenomicRanges/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicRanges'
    finding HTML links ... done
    DelegatingGenomicRanges-class           html  
    GNCList-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:46: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:47: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:48: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:49: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:55: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GNCList-class.Rd:79: file link 'NCLists' in package 'IRanges' does not exist and so has been treated as a topic
    GPos-class                              html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:73: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:74: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:74: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:77: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:92: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:94: file link 'UnstitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:95: file link 'StitchedIPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:112: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:132: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:133: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:134: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:136: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:148: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:150: file link 'seqlengths' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:151: file link 'isCircular' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:152: file link 'genome' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:202: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:225: file link 'IPos' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:254: file link 'snpsBySeqname' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:255: file link 'snpsByOverlaps' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:256: file link 'snpsById' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:257: file link 'SNPlocs' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GPos-class.Rd:260: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    GRanges-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:100: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:102: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:104: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:106: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:124: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:128: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:183: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:189: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:289: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:313: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:356: file link 'ManyToOneGrouping' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:371: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:408: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:436: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:472: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:473: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:476: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:476: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:485: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:493: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:530: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/GRanges-class.Rd:530: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
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    GRangesList-class                       html  
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    absoluteRanges                          html  
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    constraint                              html  
    coverage-methods                        html  
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    findOverlaps-methods                    html  
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    genomic-range-squeezers                 html  
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    genomicvars                             html  
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    intra-range-methods                     html  
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:87: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:91: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/intra-range-methods.Rd:160: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
    makeGRangesFromDataFrame                html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:122: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:144: file link 'getTable' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesFromDataFrame.Rd:148: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    makeGRangesListFromDataFrame            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:69: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:142: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:145: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:158: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/nearest-methods.Rd:159: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    phicoef                                 html  
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:45: file link 'punion' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:45: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:46: file link 'psetdiff' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:46: file link 'pgap' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:47: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:155: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:156: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/setops-methods.Rd:167: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    strand-utils                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:52: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.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-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:65: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.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-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/strand-utils.Rd:96: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
    tile-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:12: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:12: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:30: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:35: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tile-methods.Rd:65: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
    tileGenome                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tileGenome.Rd:68: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpM3BIEq/R.INSTALL1d7493e6e63/GenomicRanges/man/tileGenome.Rd:70: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** 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 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.38.0.zip
* DONE (GenomicRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GenomicRanges' successfully unpacked and MD5 sums checked

Tests output

GenomicRanges.Rcheck/tests_i386/run_unitTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
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, 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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Wed Apr 15 03:33:54 2020 
*********************************************** 
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 71 test functions, 0 errors, 0 failures
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  38.95    0.29   41.12

GenomicRanges.Rcheck/tests_x64/run_unitTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
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, 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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Wed Apr 15 03:34:35 2020 
*********************************************** 
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 71 test functions, 0 errors, 0 failures
Number of test functions: 71 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  41.23    0.15   41.39

Example timings

GenomicRanges.Rcheck/examples_i386/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class0.500.020.52
GPos-class37.92 4.6143.56
GRanges-class0.950.141.09
GRangesFactor-class0.400.090.50
GRangesList-class0.410.000.41
GenomicRanges-comparison0.220.000.22
absoluteRanges0.860.120.98
constraint0.830.040.86
coverage-methods0.250.000.25
findOverlaps-methods1.040.001.05
genomic-range-squeezers000
genomicvars44.7511.3656.11
inter-range-methods2.240.282.51
intra-range-methods0.480.000.49
makeGRangesFromDataFrame 0.44 0.0310.67
makeGRangesListFromDataFrame0.080.000.08
nearest-methods0.580.000.57
phicoef000
setops-methods2.820.002.83
strand-utils0.080.000.08
tile-methods0.080.000.08
tileGenome0.270.000.26

GenomicRanges.Rcheck/examples_x64/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class0.640.020.65
GPos-class34.76 4.4839.33
GRanges-class0.860.110.97
GRangesFactor-class0.560.000.56
GRangesList-class0.470.000.47
GenomicRanges-comparison0.240.000.23
absoluteRanges0.890.080.97
constraint0.960.031.00
coverage-methods0.280.000.28
findOverlaps-methods1.20.01.2
genomic-range-squeezers000
genomicvars45.9112.2358.14
inter-range-methods2.410.282.69
intra-range-methods0.510.000.51
makeGRangesFromDataFrame 0.50 0.0011.72
makeGRangesListFromDataFrame0.110.000.11
nearest-methods0.70.00.7
phicoef000
setops-methods3.950.003.95
strand-utils0.10.00.1
tile-methods0.090.000.09
tileGenome0.310.040.35