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Last data update: 2014.03.03

GenomicRanges

Package: GenomicRanges
Title: Representation and manipulation of genomic intervals and
variables defined along a genome
Description: The ability to efficiently represent and manipulate genomic
annotations and alignments is playing a central role when it comes
to analyzing high-throughput sequencing data (a.k.a. NGS data).
The GenomicRanges package defines general purpose containers for
storing and manipulating genomic intervals and variables defined along
a genome. More specialized containers for representing and manipulating
short alignments against a reference genome, or a matrix-like
summarization of an experiment, are defined in the GenomicAlignments
and SummarizedExperiment packages respectively. Both packages build
on top of the GenomicRanges infrastructure.
Version: 1.24.2
Encoding: UTF-8
Author: P. Aboyoun, H. PagÃ¨s, and M. Lawrence
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
GenomeAnnotation
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.17.5), S4Vectors (>=
0.9.47), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.1.20)
Imports: utils, stats, XVector
LinkingTo: S4Vectors, IRanges
Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>=
2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>=
0.1.5), Matrix, GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db,
org.Sc.sgd.db, pasilla, pasillaBamSubset,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
License: Artistic-2.0
Collate: utils.R phicoef.R transcript-utils.R constraint.R
strand-utils.R range-squeezers.R GenomicRanges-class.R
GenomicRanges-comparison.R GRanges-class.R GPos-class.R
DelegatingGenomicRanges-class.R GNCList-class.R
GenomicRangesList-class.R GRangesList-class.R
makeGRangesFromDataFrame.R RangedData-methods.R
findOverlaps-methods.R intra-range-methods.R
inter-range-methods.R coverage-methods.R setops-methods.R
nearest-methods.R absoluteRanges.R tileGenome.R tile-methods.R
genomicvars.R zzz.R
NeedsCompilation: yes
Packaged: 2016-06-15 02:21:39 UTC; biocbuild

● BiocViews: Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing
● 2 images, 22 functions, 0 datasets
● Reverse Depends: 144

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomicRanges' ...
** 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_GenomicRanges.c -o R_init_GenomicRanges.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 transcript_utils.c -o transcript_utils.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicRanges'
    finding HTML links ... done
    DelegatingGenomicRanges-class           html  
    GNCList-class                           html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
    GPos-class                              html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:74: missing file link 'seqlevels'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:76: missing file link 'seqlengths'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:77: missing file link 'isCircular'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:78: missing file link 'genome'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:128: missing file link 'Vector'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:157: missing file link 'snpsBySeqname'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:158: missing file link 'snpsByOverlaps'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:159: missing file link 'snpsById'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:160: missing file link 'SNPlocs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GPos-class.Rd:163: missing file link 'SummarizedExperiment'
    GRanges-class                           html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:89: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:91: missing file link 'IRanges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:93: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:95: missing file link 'DataFrame'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:113: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:117: missing file link 'IRanges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:121: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:135: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:228: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:234: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:251: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:514: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:515: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:518: missing file link 'IRanges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:518: missing file link 'DNAStringSet'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:528: missing file link 'DataFrame'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:565: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:567: missing file link 'Vector'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:567: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRanges-class.Rd:568: missing file link 'DataFrame'
    GRangesList-class                       html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRangesList-class.Rd:205: missing file link 'IRangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRangesList-class.Rd:208: missing file link 'RangedDataList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GRangesList-class.Rd:359: missing file link 'RleList-class'
    GenomicRanges-comparison                html  
    GenomicRangesList-class                 html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/GenomicRangesList-class.Rd:20: missing file link 'List'
    absoluteRanges                          html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/absoluteRanges.Rd:39: missing file link 'seqlengths'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/absoluteRanges.Rd:41: missing file link 'seqlengths'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/absoluteRanges.Rd:50: missing file link 'IRanges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/absoluteRanges.Rd:65: missing file link 'IRanges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/absoluteRanges.Rd:83: missing file link 'IRanges'
    constraint                              html  
    coverage-methods                        html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:12: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:18: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:19: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:45: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:54: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:67: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:71: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:82: missing file link 'RleList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:90: missing file link 'coverage'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/coverage-methods.Rd:95: missing file link 'RleList'
    findOverlaps-methods                    html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:26: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:29: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:30: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:31: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:99: missing file link 'Hits'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/findOverlaps-methods.Rd:113: missing file link 'findOverlaps'
    genomicvars                             html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:20: missing file link 'RleList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:49: missing file link 'RleList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:60: missing file link 'RleList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:76: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:87: missing file link 'RleList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/genomicvars.Rd:101: missing file link 'RleList'
    inter-range-methods                     html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/inter-range-methods.Rd:95: missing file link 'reduce'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/inter-range-methods.Rd:103: missing file link 'gaps'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/inter-range-methods.Rd:134: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/inter-range-methods.Rd:142: missing file link 'endoapply'
    intra-range-methods                     html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:48: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:49: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:102: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:106: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:110: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:178: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/intra-range-methods.Rd:180: missing file link 'endoapply'
    makeGRangesFromDataFrame                html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: missing file link 'DataFrame'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: missing file link 'DataFrame'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:120: missing file link 'DataFrame'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:134: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:142: missing file link 'getTable'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:146: missing file link 'DataFrame'
    nearest-methods                         html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:60: missing file link 'Hits'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:62: missing file link 'Hits'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:135: missing file link 'Hits'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:138: missing file link 'Hits'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:151: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/nearest-methods.Rd:152: missing file link 'Hits'
    phicoef                                 html  
    range-squeezers                         html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:18: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:30: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:31: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:32: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:33: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:55: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:56: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:57: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:58: missing file link 'GAlignmentsList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:64: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:65: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:78: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:81: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:97: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:99: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:102: missing file link 'GAlignments'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:103: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/range-squeezers.Rd:104: missing file link 'GAlignmentsList'
    setops-methods                          html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'punion'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'pintersect'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'psetdiff'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'pgap'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:47: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'Ranges'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'RangesList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/setops-methods.Rd:167: missing file link 'mendoapply'
    strand-utils                            html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/strand-utils.Rd:52: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/strand-utils.Rd:64: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/strand-utils.Rd:65: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/strand-utils.Rd:73: missing file link 'Rle'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/strand-utils.Rd:96: missing file link 'Rle'
    tile-methods                            html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tile-methods.Rd:9: missing file link 'tile'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tile-methods.Rd:24: missing file link 'tile'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tile-methods.Rd:29: missing file link 'tile'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tile-methods.Rd:50: missing file link 'tile'
    tileGenome                              html  
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tileGenome.Rd:68: missing file link 'IntegerList'
Rd warning: /tmp/RtmpCeC3Td/R.INSTALL5c6a66d09f8b/GenomicRanges/man/tileGenome.Rd:70: missing file link 'Views'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)
Making 'packages.html' ... done