GenomicAlignments

Package: GenomicAlignments
Title: Representation and manipulation of short genomic alignments
Description: Provides efficient containers for storing and manipulating
short genomic alignments (typically obtained by aligning short reads
to a reference genome). This includes read counting, computing the
coverage, junction detection, and working with the nucleotide content
of the alignments.
Version: 1.8.3
Encoding: UTF-8
Author: Hervé Pagès, Valerie Obenchain, Martin Morgan
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
SNP, Coverage, Alignment
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
0.9.40), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.1.20),
GenomicRanges (>= 1.24.2), SummarizedExperiment (>= 0.3.1),
Biostrings (>= 2.37.1), Rsamtools (>= 1.21.4)
Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
LinkingTo: S4Vectors, IRanges
Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,
DESeq2, edgeR, RUnit, BiocStyle
License: Artistic-2.0
Collate: cigar-utils.R GAlignments-class.R GAlignmentPairs-class.R
GAlignmentsList-class.R GappedReads-class.R
OverlapEncodings-class.R findMateAlignment.R readGAlignments.R
junctions-methods.R sequenceLayer.R pileLettersAt.R
stackStringsFromBam.R intra-range-methods.R coverage-methods.R
setops-methods.R findOverlaps-methods.R
coordinate-mapping-methods.R encodeOverlaps-methods.R
findCompatibleOverlaps-methods.R summarizeOverlaps-methods.R
findSpliceOverlaps-methods.R zzz.R
Video: https://www.youtube.com/watch?v=2KqBSbkfhRo ,
https://www.youtube.com/watch?v=3PK_jx44QTs
NeedsCompilation: yes
Packaged: 2016-06-16 04:05:54 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c cigar_utils.c -o cigar_utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include"   -fpic  -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/GenomicAlignments/libs
** 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: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:191: missing file link 'Seqinfo'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:276: missing file link 'IRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:344: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:345: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:377: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentPairs-class.Rd:378: missing file link 'GRangesList'
    GAlignments-class                       html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:164: missing file link 'Rle'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:176: missing file link 'Rle'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:218: missing file link 'Seqinfo'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:270: missing file link 'IRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:286: missing file link 'RangesList'
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Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:292: missing file link 'CompressedIRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:334: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:340: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:382: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:382: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:415: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:416: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignments-class.Rd:419: missing file link 'CompressedIRangesList'
    GAlignmentsList-class                   html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentsList-class.Rd:137: missing file link 'Seqinfo'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentsList-class.Rd:178: missing file link 'IRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentsList-class.Rd:196: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentsList-class.Rd:292: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GAlignmentsList-class.Rd:293: missing file link 'GRangesList'
    GappedReads-class                       html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/GappedReads-class.Rd:43: missing file link 'DNAStringSet'
    OverlapEncodings-class                  html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/OverlapEncodings-class.Rd:234: missing file link 'compare'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/OverlapEncodings-class.Rd:238: missing file link 'GRangesList'
    cigar-utils                             html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:133: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:135: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:139: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:189: missing file link 'solveUserSEW'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:221: missing file link 'CompressedRleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:229: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:230: missing file link 'CompressedIRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:233: missing file link 'SimpleIRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:234: missing file link 'CompressedIRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:289: missing file link 'IRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:290: missing file link 'RleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/cigar-utils.Rd:292: missing file link 'coverage'
    coordinate-mapping-methods              html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coordinate-mapping-methods.Rd:25: missing file link 'mapToTranscripts'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coordinate-mapping-methods.Rd:144: missing file link 'mapToTranscripts'
    coverage-methods                        html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:17: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:19: missing file link 'coverage'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:20: missing file link 'RangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:22: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:23: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:46: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:49: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:53: missing file link 'coverage'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:65: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:70: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:84: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:92: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:97: missing file link 'RleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:103: missing file link 'coverage'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:108: missing file link 'RleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/coverage-methods.Rd:114: missing file link 'BamFile'
    encodeOverlaps-methods                  html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:55: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:89: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:97: missing file link 'RangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:97: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:100: missing file link 'Hits'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:101: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:105: missing file link 'queryLength'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:106: missing file link 'subjectLength'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:125: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:192: missing file link 'Hits'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:198: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:203: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/encodeOverlaps-methods.Rd:206: missing file link 'findOverlaps'
    findCompatibleOverlaps-methods          html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:37: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:49: missing file link 'Hits'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findCompatibleOverlaps-methods.Rd:69: missing file link 'GRangesList'
    findMateAlignment                       html  
    findOverlaps-methods                    html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:22: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:23: missing file link 'RangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:25: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:26: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:51: missing file link 'findOverlaps'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:74: missing file link 'Hits'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findOverlaps-methods.Rd:80: missing file link 'findOverlaps'
    findSpliceOverlaps-methods              html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:37: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:38: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:46: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:49: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:58: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:61: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:68: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:94: missing file link 'Hits'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:117: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/findSpliceOverlaps-methods.Rd:122: missing file link 'BamFile'
    intra-range-methods                     html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/intra-range-methods.Rd:47: missing file link 'solveUserSEW'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/intra-range-methods.Rd:62: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/intra-range-methods.Rd:66: missing file link 'Ranges'
    junctions-methods                       html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:80: missing file link 'IntegerList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:85: missing file link 'BSgenome'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:88: missing file link 'getBSgenome'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:91: missing file link 'getBSgenome'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:144: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:151: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:161: missing file link 'IntegerList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:180: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:247: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:251: missing file link 'IntegerList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:254: missing file link 'getBSgenome'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:257: missing file link 'BSgenome'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/junctions-methods.Rd:261: missing file link 'List'
    pileLettersAt                           html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:13: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:14: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:23: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:24: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:29: missing file link 'Rle'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:43: missing file link 'GPos'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:47: missing file link 'GPos'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:49: missing file link 'GPos'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:50: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:51: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:53: missing file link 'GPos'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:64: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:82: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/pileLettersAt.Rd:85: missing file link 'GPos'
    readGAlignments                         html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:45: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:46: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:63: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:66: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:103: missing file link 'Rle'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:117: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:124: missing file link 'SimpleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:127: missing file link 'SimpleList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:155: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:164: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:208: missing file link 'BamFile'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:252: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/readGAlignments.Rd:258: missing file link 'RangesList'
    sequenceLayer                           html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/sequenceLayer.Rd:120: missing file link 'extractAt'
    setops-methods                          html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/setops-methods.Rd:14: missing file link 'pintersect'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/setops-methods.Rd:15: missing file link 'Ranges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/setops-methods.Rd:17: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/setops-methods.Rd:18: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/setops-methods.Rd:29: missing file link 'GRanges'
    stackStringsFromBam                     html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:40: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:41: missing file link 'RangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:42: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:63: missing file link 'stackStrings'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:65: missing file link 'stackStrings'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:69: missing file link 'alphabetFrequency'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:86: missing file link 'stackStrings'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:97: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:98: missing file link 'BStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:101: missing file link 'alphabetFrequency'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:131: missing file link 'stackStrings'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:133: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/stackStringsFromBam.Rd:135: missing file link 'alphabetFrequency'
    summarizeOverlaps-methods               html  
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:83: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:84: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:86: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:90: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:94: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:98: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:100: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:101: missing file link 'BamFileList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:104: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:107: missing file link 'BamViews'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:216: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:251: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:252: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:253: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:255: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:260: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:262: missing file link 'GRanges'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:285: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:316: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:321: missing file link 'BamFileList'
Rd warning: /tmp/Rtmpdyz2Uk/R.INSTALL62ac3c999a11/GenomicAlignments/man/summarizeOverlaps-methods.Rd:321: missing file link 'BamViews'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicAlignments)
Making 'packages.html' ... done