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CHECK report for GenomicAlignments on tokay2

This page was generated on 2018-10-17 08:37:59 -0400 (Wed, 17 Oct 2018).

Package 592/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.16.0
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenomicAlignments
Branch: RELEASE_3_7
Last Commit: db032a4
Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicAlignments
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicAlignments.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicAlignments_1.16.0.tar.gz
StartedAt: 2018-10-17 02:15:09 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:26:11 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 661.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicAlignments.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicAlignments.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicAlignments_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.16.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  'SummarizedExperiment' 'Biostrings' 'Rsamtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicAlignments' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:168: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:278: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:355: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:389: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:390: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:173: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:185: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:279: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:295: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:300: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:301: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:343: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:349: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:375: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:427: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:428: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:431: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:174: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:192: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:260: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:291: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:292: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GappedReads-class.Rd:43: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/OverlapEncodings-class.Rd:112: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/OverlapEncodings-class.Rd:273: file link 'pcompare' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/OverlapEncodings-class.Rd:277: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:133: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:135: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:139: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:189: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:221: file link 'CompressedRleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:229: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:230: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:233: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:233: file link 'SimpleIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:234: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:289: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:290: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/cigar-utils.Rd:292: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: file link 'mapToTranscripts' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:15: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:17: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:19: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:20: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:22: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:23: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:46: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:53: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:65: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:70: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:84: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:92: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:97: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:103: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:108: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/coverage-methods.Rd:114: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:50: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:83: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:95: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:96: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:100: file link 'queryLength' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:101: file link 'subjectLength' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:120: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:186: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:192: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:197: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/encodeOverlaps-methods.Rd:200: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/findCompatibleOverlaps-methods.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-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:49: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:135: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Biostrings' 'Rsamtools'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'BSgenome' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'Biostrings:::.normarg_padding.letter'
  'Rsamtools:::.BamViews_delegate' 'Rsamtools:::.findMateWithinGroups'
  'Rsamtools:::.load_bamcols_from_scanBam_res'
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'updateObject' and siglist 'GAlignments'
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
Objects in \usage without \alias in documentation object 'intra-range-methods':
  '\S4method{narrow}{GAlignmentsList}'

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-3.7-bioc/R/library/GenomicAlignments/libs/i386/GenomicAlignments.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
junctions-methods          16.24   1.39   19.39
readGAlignments            12.31   0.55   12.86
sequenceLayer               9.32   0.59    9.90
coordinate-mapping-methods  8.64   0.43    9.08
summarizeOverlaps-methods   7.97   0.36   17.81
findSpliceOverlaps-methods  6.01   0.15    6.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
junctions-methods          14.74   1.40   17.33
readGAlignments             9.14   0.41    9.55
coordinate-mapping-methods  6.88   0.35    7.58
sequenceLayer               6.42   0.35    6.77
summarizeOverlaps-methods   6.00   0.20   31.55
findSpliceOverlaps-methods  4.96   0.14    5.09
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.

Installation output

GenomicAlignments.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GenomicAlignments_1.16.0.tar.gz && rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments_1.16.0.zip && rm GenomicAlignments_1.16.0.tar.gz GenomicAlignments_1.16.0.zip
###
##############################################################################
##############################################################################


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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1369k  100 1369k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 20.5M

install for i386

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
         ^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
    range_buf1 = range_buf2->elts[*f_elt - 1];
                           ^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                      ^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                ^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    flag_elt++;
            ^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:887:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
   buf_offset += sprintf(cigar_buf + buf_offset,
                 ^
cigar_utils.c:855:7: note: 'OP' was declared here
  char OP /* Operation */;
       ^
cigar_utils.c:879:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
    OPL -= Lwidth;
        ^
cigar_utils.c:854:17: note: 'OPL' was declared here
  int offset, n, OPL /* Operation Length */;
                 ^
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1071:17: warning: 'OP' may be used uninitialized in this function [-Wmaybe-uninitialized]
   buf_offset += sprintf(cigar_buf + buf_offset,
                 ^
cigar_utils.c:1039:7: note: 'OP' was declared here
  char OP /* Operation */;
       ^
cigar_utils.c:1063:8: warning: 'OPL' may be used uninitialized in this function [-Wmaybe-uninitialized]
    OPL -= Lqwidth;
        ^
cigar_utils.c:1038:17: note: 'OPL' was declared here
  int offset, n, OPL /* Operation Length */;
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_delete_at(out, out_nelt0, j1 * nrow);
  ^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicAlignments'
    finding HTML links ... done
    GAlignmentPairs-class                   html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:168: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:278: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:355: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:357: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:389: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentPairs-class.Rd:390: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    GAlignments-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:173: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:185: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:279: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:295: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:300: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:301: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:343: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:349: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:375: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:394: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:427: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:428: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignments-class.Rd:431: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    GAlignmentsList-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:174: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:192: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:260: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/GAlignmentsList-class.Rd:291: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/junctions-methods.Rd:261: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
    pileLettersAt                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:13: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:14: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:23: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:51: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:53: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:64: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:64: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/pileLettersAt.Rd:82: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
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    readGAlignments                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:45: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:46: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:63: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:66: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:103: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:117: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:124: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:127: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:155: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:164: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:208: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:252: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/readGAlignments.Rd:258: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    sequenceLayer                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/sequenceLayer.Rd:120: file link 'extractAt' in package 'Biostrings' does not exist and so has been treated as a topic
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/setops-methods.Rd:14: file link 'pintersect' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/setops-methods.Rd:15: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/setops-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/setops-methods.Rd:18: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/setops-methods.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    stackStringsFromBam                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:40: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:41: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:63: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:65: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:69: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:86: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:97: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:98: file link 'BStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:101: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:131: file link 'stackStrings' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:133: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/stackStringsFromBam.Rd:135: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
    summarizeOverlaps-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamFileList' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp4WZpXY/R.INSTALLa3c465d237/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
         ^
cigar_utils.c:658:27: warning: 'range_buf2' may be used uninitialized in this function [-Wmaybe-uninitialized]
    range_buf1 = range_buf2->elts[*f_elt - 1];
                           ^
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                      ^
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                ^
cigar_utils.c:670:12: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    flag_elt++;
            ^
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_delete_at(out, out_nelt0, j1 * nrow);
  ^
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.16.0.zip
* DONE (GenomicAlignments)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GenomicAlignments' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GenomicAlignments.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomicAlignments") || stop("unable to load GenomicRanges package")
Loading required package: GenomicAlignments
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

Loading required package: S4Vectors
Loading required package: stats4

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
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> GenomicAlignments:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 02:24:34 2018 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicAlignments RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
Warning message:
In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
    4 alignments with ambiguous pairing were dumped.
    Use 'getDumpedAlignments()' to retrieve them from the dump environment.
> 
> proc.time()
   user  system elapsed 
  23.53    0.79  148.23

GenomicAlignments.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomicAlignments") || stop("unable to load GenomicRanges package")
Loading required package: GenomicAlignments
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

Loading required package: S4Vectors
Loading required package: stats4

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
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> GenomicAlignments:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 02:25:14 2018 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicAlignments RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
Warning message:
In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
    4 alignments with ambiguous pairing were dumped.
    Use 'getDumpedAlignments()' to retrieve them from the dump environment.
> 
> proc.time()
   user  system elapsed 
  22.21    0.54   38.84

Example timings

GenomicAlignments.Rcheck/examples_i386/GenomicAlignments-Ex.timings

nameusersystemelapsed
GAlignmentPairs-class0.760.040.81
GAlignments-class0.330.080.41
GAlignmentsList-class2.340.052.40
GappedReads-class0.090.000.09
OverlapEncodings-class1.520.001.51
cigar-utils0.260.000.27
coordinate-mapping-methods8.640.439.08
coverage-methods2.130.132.25
encodeOverlaps-methods0.020.000.01
findCompatibleOverlaps-methods1.040.061.11
findMateAlignment0.10.00.1
findOverlaps-methods0.360.000.36
findSpliceOverlaps-methods6.010.156.17
intra-range-methods0.310.000.32
junctions-methods16.24 1.3919.39
pileLettersAt0.450.080.53
readGAlignments12.31 0.5512.86
sequenceLayer9.320.599.90
setops-methods0.060.020.08
stackStringsFromBam1.630.031.65
summarizeOverlaps-methods 7.97 0.3617.81

GenomicAlignments.Rcheck/examples_x64/GenomicAlignments-Ex.timings

nameusersystemelapsed
GAlignmentPairs-class1.670.071.75
GAlignments-class0.390.040.42
GAlignmentsList-class3.880.284.15
GappedReads-class0.150.000.16
OverlapEncodings-class1.740.001.73
cigar-utils0.150.010.17
coordinate-mapping-methods6.880.357.58
coverage-methods2.640.072.72
encodeOverlaps-methods0.030.000.03
findCompatibleOverlaps-methods1.000.051.04
findMateAlignment0.110.000.11
findOverlaps-methods0.360.060.43
findSpliceOverlaps-methods4.960.145.09
intra-range-methods0.310.000.31
junctions-methods14.74 1.4017.33
pileLettersAt0.560.010.57
readGAlignments9.140.419.55
sequenceLayer6.420.356.77
setops-methods0.080.000.08
stackStringsFromBam1.20.01.2
summarizeOverlaps-methods 6.00 0.2031.55