| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:23:37 -0400 (Thu, 12 Apr 2018).
| Package 562/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicAlignments 1.14.2 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GenomicAlignments |
| Version: 1.14.2 |
| Command: rm -rf GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && mkdir GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.14.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz |
| StartedAt: 2018-04-12 00:17:14 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:26:04 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 529.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicAlignments.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && mkdir GenomicAlignments.buildbin-libdir GenomicAlignments.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.14.2.tar.gz >GenomicAlignments.Rcheck\00install.out 2>&1 && cp GenomicAlignments.Rcheck\00install.out GenomicAlignments-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicAlignments.buildbin-libdir --install="check:GenomicAlignments-install.out" --force-multiarch --no-vignettes --timings GenomicAlignments_1.14.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.14.2'
* 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-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:164: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:274: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:352: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:353: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:385: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:386: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:171: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:183: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:277: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:293: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:298: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:299: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:341: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:347: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:422: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:423: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:426: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:178: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:196: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:292: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:293: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GappedReads-class.Rd:43: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:111: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:272: missing file link 'pcompare'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:276: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:133: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:135: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:139: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:189: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:221: missing file link 'CompressedRleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:229: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:230: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'SimpleIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:234: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:290: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:292: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: missing file link 'mapToTranscripts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: missing file link 'mapToTranscripts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:17: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:19: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:22: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:23: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:46: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:49: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:53: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:65: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:70: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:84: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:92: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:97: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:103: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:108: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:114: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:50: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:95: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:99: missing file link 'queryLength'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:100: missing file link 'subjectLength'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:119: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:185: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:191: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:196: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:199: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:37: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:49: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:69: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:22: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:26: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:51: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:74: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:80: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:37: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:38: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:46: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:49: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:58: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:61: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:68: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:122: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:127: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:47: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:62: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:66: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:80: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:85: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:88: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:91: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:144: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:151: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:161: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:180: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:251: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:254: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:257: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:261: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:13: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:14: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:23: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:24: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:29: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:43: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:47: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:49: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:50: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:51: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:53: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:82: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:85: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:45: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:46: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:63: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:66: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:103: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:117: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:124: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:127: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:155: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:164: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:208: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:252: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:258: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/sequenceLayer.Rd:120: missing file link 'extractAt'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:14: missing file link 'pintersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:15: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:18: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:29: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:40: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:41: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:42: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:63: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:65: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:69: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:86: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:97: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:98: missing file link 'BStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:101: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:131: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:133: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:135: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamViews'
See 'C:/Users/biocbuild/bbs-3.6-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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.buildbin-libdir/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
junctions-methods 18.94 1.33 26.03
readGAlignments 10.09 0.19 10.29
coordinate-mapping-methods 8.81 0.23 9.04
sequenceLayer 6.81 0.43 7.31
findSpliceOverlaps-methods 6.13 0.14 7.83
summarizeOverlaps-methods 5.68 0.25 13.69
GAlignmentsList-class 4.98 0.10 5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
junctions-methods 20.44 1.05 21.54
readGAlignments 12.83 0.51 13.34
sequenceLayer 12.08 0.61 12.69
summarizeOverlaps-methods 9.23 0.28 21.15
coordinate-mapping-methods 7.66 0.30 7.95
findSpliceOverlaps-methods 7.25 0.22 7.46
* 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.
GenomicAlignments.Rcheck/00install.out
install for i386
* installing *source* package 'GenomicAlignments' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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/g++ -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/i386
** R
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:164: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:274: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:352: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:353: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:385: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentPairs-class.Rd:386: missing file link 'GRangesList'
GAlignments-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:171: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:183: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:277: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:293: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:298: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:299: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:341: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:347: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:389: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:422: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:423: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignments-class.Rd:426: missing file link 'CompressedIRangesList'
GAlignmentsList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:178: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:196: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:292: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GAlignmentsList-class.Rd:293: missing file link 'GRangesList'
GappedReads-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/GappedReads-class.Rd:43: missing file link 'DNAStringSet'
OverlapEncodings-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:111: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:272: missing file link 'pcompare'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/OverlapEncodings-class.Rd:276: missing file link 'GRangesList'
cigar-utils html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:133: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:135: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:139: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:189: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:221: missing file link 'CompressedRleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:229: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:230: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'SimpleIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:234: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:290: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/cigar-utils.Rd:292: missing file link 'coverage'
coordinate-mapping-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: missing file link 'mapToTranscripts'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: missing file link 'mapToTranscripts'
coverage-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:17: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:19: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:22: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:23: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:46: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:49: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:53: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:65: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:70: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:84: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:92: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:97: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:103: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:108: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/coverage-methods.Rd:114: missing file link 'BamFile'
encodeOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:50: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:91: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:95: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:99: missing file link 'queryLength'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:100: missing file link 'subjectLength'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:119: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:185: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:191: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:196: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/encodeOverlaps-methods.Rd:199: missing file link 'findOverlaps'
findCompatibleOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:37: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:49: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:69: missing file link 'GRangesList'
findMateAlignment html
findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:22: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:26: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:51: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:74: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findOverlaps-methods.Rd:80: missing file link 'findOverlaps'
findSpliceOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:37: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:38: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:46: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:49: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:58: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:61: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:68: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:122: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:127: missing file link 'BamFile'
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:47: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:62: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/intra-range-methods.Rd:66: missing file link 'Ranges'
junctions-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:80: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:85: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:88: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:91: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:144: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:151: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:161: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:180: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:251: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:254: missing file link 'getBSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:257: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/junctions-methods.Rd:261: missing file link 'List'
pileLettersAt html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:13: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:14: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:23: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:24: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:29: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:43: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:47: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:49: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:50: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:51: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:53: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:82: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/pileLettersAt.Rd:85: missing file link 'GPos'
readGAlignments html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:45: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:46: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:63: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:66: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:103: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:117: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:124: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:127: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:155: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:164: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:208: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:252: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/readGAlignments.Rd:258: missing file link 'RangesList'
sequenceLayer html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/sequenceLayer.Rd:120: missing file link 'extractAt'
setops-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:14: missing file link 'pintersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:15: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:17: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:18: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/setops-methods.Rd:29: missing file link 'GRanges'
stackStringsFromBam html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:40: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:41: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:42: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:63: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:65: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:69: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:86: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:97: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:98: missing file link 'BStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:101: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:131: missing file link 'stackStrings'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:133: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/stackStringsFromBam.Rd:135: missing file link 'alphabetFrequency'
summarizeOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: missing file link 'BamViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:215: missing file link 'ScanBamParam'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:250: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:254: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:259: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:261: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:284: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:315: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamFileList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpot2PV7/R.INSTALL1088b0766ad/GenomicAlignments/man/summarizeOverlaps-methods.Rd:320: missing file link 'BamViews'
** 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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/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/g++ -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicAlignments.buildbin-libdir/GenomicAlignments/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicAlignments' as GenomicAlignments_1.14.2.zip
* DONE (GenomicAlignments)
In R CMD INSTALL
In R CMD INSTALL
|
GenomicAlignments.Rcheck/tests_i386/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
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 -- Thu Apr 12 00:24:57 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
28.89 0.53 48.45
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GenomicAlignments.Rcheck/tests_x64/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:base':
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 -- Thu Apr 12 00:25:50 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
35.71 0.43 53.01
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GenomicAlignments.Rcheck/examples_i386/GenomicAlignments-Ex.timings
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GenomicAlignments.Rcheck/examples_x64/GenomicAlignments-Ex.timings
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