R Graphical Manual

Browse All

Last data update: 2014.03.03

GenomicFeatures

Package: GenomicFeatures
Title: Tools for making and manipulating transcript centric annotations
Version: 1.24.3
Encoding: UTF-8
Author: M. Carlson, H. PagÃ¨s, P. Aboyoun, S. Falcon, M. Morgan,
D. Sarkar, M. Lawrence
License: Artistic-2.0
Description: A set of tools and methods for making and manipulating
transcript centric annotations. With these tools the user can
easily download the genomic locations of the transcripts, exons
and cds of a given organism, from either the UCSC Genome
Browser or a BioMart database (more sources will be supported
in the future). This information is then stored in a local
database that keeps track of the relationship between
transcripts, exons, cds and genes. Flexible methods are
provided for extracting the desired features in a convenient
format.
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.47), IRanges (>=
2.3.21), GenomeInfoDb (>= 1.5.16), GenomicRanges (>= 1.21.32),
AnnotationDbi (>= 1.33.15)
Imports: methods, utils, stats, tools, DBI, RSQLite, RCurl, XVector,
Biostrings (>= 2.23.3), rtracklayer (>= 1.29.24), biomaRt (>=
2.17.1), Biobase (>= 2.15.1)
Suggests: org.Mm.eg.db, org.Hs.eg.db, BSgenome,
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene,
SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments, RUnit, BiocStyle, knitr
Collate: utils.R TxDb-SELECT-helpers.R Ensembl.utils.R
findCompatibleMarts.R TxDb-class.R FeatureDb-class.R makeTxDb.R
makeTxDbFromUCSC.R makeTxDbFromBiomart.R makeTxDbFromGRanges.R
makeTxDbFromGFF.R makeFeatureDbFromUCSC.R mapIdsToRanges.R
id2name.R transcripts.R transcriptsBy.R transcriptsByOverlaps.R
transcriptLengths.R disjointExons.R features.R microRNAs.R
extractTranscriptSeqs.R extractUpstreamSeqs.R
getPromoterSeq-methods.R makeTxDbPackage.R select-methods.R
nearest-methods.R transcriptLocs2refLocs.R
coordinate-mapping-methods.R coverageByTranscript.R zzz.R
VignetteBuilder: knitr
biocViews: Genetics, Infrastructure, Annotation, Sequencing,
GenomeAnnotation
NeedsCompilation: no
Packaged: 2016-06-21 02:07:09 UTC; biocbuild

● BiocViews: Annotation, Genetics, GenomeAnnotation, Infrastructure, Sequencing
● 0 images, 28 functions, 1 datasets
● Reverse Depends: 47

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFeatures'
    finding HTML links ... done
    DEFAULT_CIRC_SEQS                       html  
    FeatureDb-class                         html  
    finding level-2 HTML links ... done

    TxDb-class                              html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/TxDb-class.Rd:61: missing file link 'Seqinfo'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/TxDb-class.Rd:102: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/TxDb-class.Rd:105: missing file link 'saveDb'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/TxDb-class.Rd:106: missing file link 'loadDb'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/TxDb-class.Rd:123: missing file link 'Seqinfo'
    as-format-methods                       html  
    coordinate-mapping-methods              html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: missing file link 'mapToAlignments'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coordinate-mapping-methods.Rd:204: missing file link 'mapToAlignments'
    coverageByTranscript                    html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:26: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:27: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:28: missing file link 'GAlignmentsList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:32: missing file link 'coverage'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:33: missing file link 'BamFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:35: missing file link 'RleList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:38: missing file link 'grglist'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:43: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:54: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:69: missing file link 'grglist'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:70: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:71: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:73: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:74: missing file link 'grglist'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:79: missing file link 'RleList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:80: missing file link 'Rle'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:97: missing file link 'RleList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:100: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:103: missing file link 'coverage'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/coverageByTranscript.Rd:109: missing file link 'findCompatibleOverlaps'
    disjointExons                           html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/disjointExons.Rd:43: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/disjointExons.Rd:54: missing file link 'GRanges'
    extractTranscriptSeqs                   html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: missing file link 'DNAString'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: missing file link 'DNAString'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: missing file link 'RangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:43: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:45: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:48: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:73: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:78: missing file link 'DNAString'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:80: missing file link 'Rle'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:83: missing file link 'Rle'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:86: missing file link 'RangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:92: missing file link 'RangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:102: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAString'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:131: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractTranscriptSeqs.Rd:134: missing file link 'RangesList'
    extractUpstreamSeqs                     html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'TwoBitFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:115: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:115: missing file link 'TwoBitFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:125: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/extractUpstreamSeqs.Rd:128: missing file link 'DNAStringSet'
    features                                html  
    getPromoterSeq-methods                  html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'BSgenome'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'FaFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: missing file link 'DNAStringSetList'
    id2name                                 html  
    makeFeatureDbFromUCSC                   html  
    makeTxDb                                html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDb.Rd:152: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDb.Rd:157: missing file link 'saveDb'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDb.Rd:158: missing file link 'loadDb'
    makeTxDbFromBiomart                     html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromBiomart.Rd:125: missing file link 'GRanges'
    makeTxDbFromGFF                         html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGFF.Rd:28: missing file link 'GFF3File'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: missing file link 'GTFFile'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGFF.Rd:63: missing file link 'Seqinfo'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGFF.Rd:93: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGFF.Rd:95: missing file link 'import'
    makeTxDbFromGRanges                     html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: missing file link 'import'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGRanges.Rd:55: missing file link 'import'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromGRanges.Rd:61: missing file link 'GRanges'
    makeTxDbFromUCSC                        html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/makeTxDbFromUCSC.Rd:83: missing file link 'GRanges'
    makeTxDbPackage                         html  
    mapIdsToRanges                          html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/mapIdsToRanges.Rd:24: missing file link 'GRangesList'
    mapRangesToIds                          html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/mapRangesToIds.Rd:25: missing file link 'DataFrame'
    microRNAs                               html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/microRNAs.Rd:32: missing file link 'GRanges'
    nearest-methods                         html  
    select-methods                          html  
    transcriptLengths                       html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptLengths.Rd:40: missing file link 'GRanges'
    transcriptLocs2refLocs                  html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: missing file link 'IntegerList'
    transcripts                             html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcripts.Rd:84: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcripts.Rd:85: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcripts.Rd:88: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcripts.Rd:121: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcripts.Rd:123: missing file link 'GRangesList'
    transcriptsBy                           html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsBy.Rd:49: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsBy.Rd:52: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsBy.Rd:54: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsBy.Rd:79: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsBy.Rd:89: missing file link 'GRangesList'
    transcriptsByOverlaps                   html  
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: missing file link 'GRanges'
Rd warning: /tmp/Rtmp6STFkC/R.INSTALL64c11f7d4ae1/GenomicFeatures/man/transcriptsByOverlaps.Rd:60: missing file link 'findOverlaps'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicFeatures)
Making 'packages.html' ... done