RIPSeeker

Package: RIPSeeker
Type: Package
Title: RIPSeeker: a statistical package for identifying
protein-associated transcripts from RIP-seq experiments
Version: 1.12.0
Date: 2013-Apr-13
Author: Yue Li
Maintainer: Yue Li <yueli@cs.toronto.edu>
Description: Infer and discriminate RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission
probability. While RIPSeeker is specifically tailored for
RIP-seq data analysis, it also provides a suite of
bioinformatics tools integrated within this self-contained
software package comprehensively addressing issues ranging from
post-alignments processing to visualization and annotation.
Depends: R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges,
GenomicRanges, SummarizedExperiment, Rsamtools,
GenomicAlignments, rtracklayer
Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures
License: GPL-2
URL: http://www.cs.utoronto.ca/~yueli/software.html
Lazyload: yes
Packaged: 2016-05-04 04:46:29 UTC; biocbuild
biocViews: Sequencing, RIPSeq
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RIPSeeker'
    finding HTML links ... done
    RIPSeeker-package                       html  
    addDummyProb                            html  
    addPseudoAlignment                      html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/addPseudoAlignment.Rd:52: missing file link 'import'
    annotateRIP                             html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/annotateRIP.Rd:21: missing file link 'GRanges'
    binCount                                html  
    combineAlignGals                        html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineAlignGals.Rd:54: missing file link 'import'
    combineRIP                              html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineRIP.Rd:58: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineRIP.Rd:70: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineRIP.Rd:95: missing file link 'import'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineRIP.Rd:95: missing file link 'reduce'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/combineRIP.Rd:95: missing file link 'countOverlaps'
    computeLogOdd                           html  
    computeRPKM                             html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'exonsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'cdsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'intronsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'fiveUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:47: missing file link 'threeUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:67: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:76: missing file link 'summarizeOverlaps'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:84: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'exonsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'cdsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'intronsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'fiveUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'threeUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'summarizeOverlaps'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'ScanBamParam'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/computeRPKM.Rd:113: missing file link 'readGAlignmentPairs'
    disambiguateMultihits                   html  
    empiricalFDR                            html  
    evalBinSize                             html  
    exportGRanges                           html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/exportGRanges.Rd:19: missing file link 'GRanges'
    galp2gal                                html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/galp2gal.Rd:50: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/galp2gal.Rd:50: missing file link 'import'
    getAlignGal                             html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:42: missing file link 'scanBamFlag'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'import'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:63: missing file link 'GAlignments'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/getAlignGal.Rd:96: missing file link 'import'
    logScoreWithControl                     html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithControl.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithControl.Rd:23: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithControl.Rd:36: missing file link 'pnorm'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithControl.Rd:44: missing file link 'GRanges'
    logScoreWithoutControl                  html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithoutControl.Rd:28: missing file link 'pnorm'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/logScoreWithoutControl.Rd:36: missing file link 'GRanges'
    mainSeek                                html  
    mainSeekSingleChrom                     html  
    nbh.GRanges                             html  
    nbh                                     html  
    nbh.integer                             html  
    nbh_chk                                 html  
    nbh_em                                  html  
    nbh_gen                                 html  
    nbh_init                                html  
    nbh_vit                                 html  
    nbm_chk                                 html  
    nbm_em                                  html  
    plotCoverage                            html  
    plotStrandedCoverage                    html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/plotStrandedCoverage.Rd:19: missing file link 'GRanges'
    randindx                                html  
    ripSeek                                 html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/ripSeek.Rd:106: missing file link 'GRangesList'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/ripSeek.Rd:108: missing file link 'GAlignments'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/ripSeek.Rd:113: missing file link 'GRangesList'
    rulebaseRIPSeek                         html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:76: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'exonsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'cdsBy'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'intronsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'fiveUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'threeUTRsByTranscript'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'summarizeOverlaps'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'ScanBamParam'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/rulebaseRIPSeek.Rd:106: missing file link 'readGAlignmentPairs'
    scoreMergedBins                         html  
    seekRIP                                 html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/seekRIP.Rd:21: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/seekRIP.Rd:25: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/seekRIP.Rd:50: missing file link 'pnorm'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/seekRIP.Rd:61: missing file link 'GRanges'
    selectBinSize                           html  
    statdis                                 html  
    viewRIP                                 html  
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:21: missing file link 'GRangesList'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:25: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:29: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:33: missing file link 'GRanges'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserSession'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:54: missing file link 'track'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:54: missing file link 'browserView'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserSession'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:80: missing file link 'track'
Rd warning: /tmp/RtmpDZDCdF/R.INSTALL3cec7b7cce36/RIPSeeker/man/viewRIP.Rd:80: missing file link 'browserView'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RIPSeeker)
Making 'packages.html' ... done