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Last data update: 2014.03.03
BSgenome

Package: BSgenome
Title: Infrastructure for Biostrings-based genome data packages and
support for efficient SNP representation
Description: Infrastructure shared by all the Biostrings-based genome data
packages
Version: 1.40.1
Encoding: UTF-8
Author: HervÃ© PagÃ¨s
Maintainer: H. PagÃ¨s <hpages@fredhutch.org>
biocViews: Genetics, Infrastructure, DataRepresentation,
SequenceMatching, Annotation, SNP
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=
0.9.36), IRanges (>= 2.1.33), GenomeInfoDb (>= 1.3.19),
GenomicRanges (>= 1.23.15), Biostrings (>= 2.35.3), rtracklayer
(>= 1.25.8)
Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
rtracklayer
Suggests: BiocInstaller, Biobase, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP141.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, hgu95av2probe, RUnit
License: Artistic-2.0
LazyLoad: yes
Collate: utils.R OnDiskLongTable-class.R OnDiskNamedSequences-class.R
SNPlocs-class.R InjectSNPsHandler-class.R XtraSNPlocs-class.R
BSgenome-class.R available.genomes.R injectSNPs.R
getSeq-methods.R bsapply.R BSgenomeViews-class.R
BSgenome-utils.R export-methods.R BSgenomeForge.R
NeedsCompilation: no
Packaged: 2016-06-16 01:42:13 UTC; biocbuild
● BiocViews: Annotation, DataRepresentation, Genetics, Infrastructure, SNP, SequenceMatching
● 0 images, 12 functions, 0 datasets
● Reverse Depends: 103
Install log

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

    BSgenome-class                          html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:46: missing file link 'GenomeDescription'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:47: missing file link 'GenomeDescription'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:58: missing file link 'DNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:59: missing file link 'MaskedDNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:68: missing file link 'length,XVector-method'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:69: missing file link 'length,MaskedXString-method'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:70: missing file link 'DNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:71: missing file link 'MaskedDNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:73: missing file link 'MaskedXString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:75: missing file link 'MaskedXString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:83: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:143: missing file link 'BSgenome.Hsapiens.UCSC.hg38'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:155: missing file link 'DNAStringSet-class'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:156: missing file link 'MaskedDNAString-class'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-class.Rd:159: missing file link 'subseq,XVector-method'
    BSgenome-utils                          html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:46: missing file link 'DNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:49: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:108: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:111: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:113: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:121: missing file link 'DataFrame'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenome-utils.Rd:133: missing file link 'matchPDict'
    BSgenomeForge                           html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeForge.Rd:75: missing file link 'XString'
    BSgenomeViews-class                     html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:120: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:135: missing file link 'alphabetFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:136: missing file link 'oligonucleotideFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:140: missing file link 'alphabetFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:144: missing file link 'oligonucleotideFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:148: missing file link 'consensusMatrix'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:179: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:215: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:241: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:245: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:246: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:249: missing file link 'seqtype'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:250: missing file link 'nchar,XStringSet-method'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:251: missing file link 'unlist,XStringSet-method'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:252: missing file link 'alphabetFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:253: missing file link 'hasOnlyBaseLetters'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:254: missing file link 'uniqueLetters'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:256: missing file link 'oligonucleotideFrequency'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:257: missing file link 'nucleotideFrequencyAt'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:258: missing file link 'consensusMatrix'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:259: missing file link 'consensusString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:271: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:274: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/BSgenomeViews-class.Rd:281: missing file link 'TxDb'
    SNPlocs-class                           html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:107: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:116: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:120: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:122: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:123: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:126: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:147: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:161: missing file link 'GPos'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:173: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:177: missing file link 'GPos'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:196: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:207: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:220: missing file link 'GPos'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/SNPlocs-class.Rd:220: missing file link 'GRanges'
    XtraSNPlocs-class                       html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:96: missing file link 'DataFrame'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:97: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:100: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:105: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:107: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:108: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:111: missing file link 'GenomicRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:125: missing file link 'subsetByOverlaps'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:137: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:139: missing file link 'DataFrame'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:140: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:146: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:152: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:160: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:165: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:169: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:173: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:177: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:184: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/XtraSNPlocs-class.Rd:193: missing file link 'GRanges'
    available.genomes                       html  
    bsapply                                 html  
    export-methods                          html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/export-methods.Rd:33: missing file link 'FastaFile'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/export-methods.Rd:33: missing file link 'TwoBitFile'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/export-methods.Rd:61: missing file link 'TwoBitFile'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/export-methods.Rd:71: missing file link 'FastaFile'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/export-methods.Rd:71: missing file link 'TwoBitFile'
    getSeq-methods                          html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:12: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:23: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:31: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:32: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:33: missing file link 'RangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:34: missing file link 'Ranges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:35: missing file link 'RangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:35: missing file link 'Ranges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:45: missing file link 'XStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:46: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:52: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:53: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:53: missing file link 'RangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:54: missing file link 'Ranges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:59: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:60: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:72: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:73: missing file link 'Ranges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:74: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:75: missing file link 'RangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:82: missing file link 'solveUserSEW'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:86: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:87: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:101: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:102: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:110: missing file link 'DNAStringSet'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:115: missing file link 'DNAStringSetList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:116: missing file link 'CharacterList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:118: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:119: missing file link 'DNAString'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:121: missing file link 'GRanges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:122: missing file link 'GRangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:122: missing file link 'RangesList'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:123: missing file link 'Ranges'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:135: missing file link 'MaskedDNAString-class'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:146: missing file link 'DNAStringSet-class'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/getSeq-methods.Rd:147: missing file link 'MaskedDNAString-class'
    injectSNPs                              html  
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/injectSNPs.Rd:113: missing file link 'letterFrequencyInSlidingView'
Rd warning: /tmp/Rtmpa0XX8n/R.INSTALL64e67b839bff/BSgenome/man/injectSNPs.Rd:114: missing file link '.inplaceReplaceLetterAt'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BSgenome)
Making 'packages.html' ... done