TFBSTools

Package: TFBSTools
Version: 1.10.3
Date: 2016-05-29
Title: Software Package for Transcription Factor Binding Site (TFBS)
Analysis
Description: TFBSTools is a package for the analysis and manipulation of
transcription factor binding sites. It includes matrices conversion
between Position Frequency Matirx (PFM),
Position Weight Matirx (PWM) and Information Content Matrix (ICM).
It can also scan putative TFBS from sequence/alignment,
query JASPAR database and provides a wrapper of
de novo motif discovery software.
Authors@R: person("Ge", "Tan", email="ge.tan09@imperial.ac.uk",
role = c("aut", "cre"))
VignetteBuilder: knitr
Imports: Biobase (>= 2.28), Biostrings (>= 2.36.4), BiocGenerics (>=
0.14.0), BiocParallel (>= 1.2.21), BSgenome (>= 1.36.3),
caTools (>= 1.17.1), CNEr (>= 1.4.0), DirichletMultinomial (>=
1.10.0), GenomeInfoDb (>= 1.6.1), GenomicRanges (>= 1.20.6),
gtools (>= 3.5.0), grid, IRanges (>= 2.2.7), methods, RSQLite (>=
1.0.0), rtracklayer (>= 1.28.10), seqLogo (>= 1.34.0),
S4Vectors (>= 0.9.25), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3),
XVector (>= 0.8.0)
Depends: R (>= 3.2.2)
Suggests: BiocStyle (>= 1.7.7), JASPAR2014 (>= 1.4.0), knitr (>= 1.11),
testthat, JASPAR2016 (>= 1.0.0)
License: GPL-2
URL: https://github.com/ge11232002/TFBSTools
BugReports: https://github.com/ge11232002/TFBSTools/issues
Type: Package
biocViews: MotifAnnotation, GeneRegulation, MotifDiscovery,
Transcription, Alignment
NeedsCompilation: yes
LazyData: yes
Collate: AllGenerics.r AllClasses.r show-methods.r util-methods.r
XMatrix-methods.r XMatrixList-methods.r SiteSet-methods.r
coercion-methods.r DB-methods.r JASPAR.R
PairwiseAlignment-methods.r ICM-methods.r PWM-methods.r
Motif-methods.r PFM-methods.r Wrappers-methods.r
DirichletMixture.r TFFM.R TFFMseqLogo.R IO.R Enrichment.R
Packaged: 2016-05-30 04:16:00 UTC; biocbuild
Author: Ge Tan [aut, cre]
Maintainer: Ge Tan <ge.tan09@imperial.ac.uk>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TFBSTools' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_TFBSTools.c -o R_init_TFBSTools.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o TFBSTools.so matrixAlignerDynamic.o R_init_TFBSTools.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/TFBSTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'seqLogo' in package 'TFBSTools'
Creating a generic function for 'colSums' from package 'base' in package 'TFBSTools'
Creating a generic function for 'rowSums' from package 'base' in package 'TFBSTools'
Creating a generic function for 'update' from package 'stats' in package 'TFBSTools'
Creating a generic function for 'as.matrix' from package 'base' in package 'TFBSTools'
** help
*** installing help indices
  converting help for package 'TFBSTools'
    finding HTML links ... done
    IUPAC2Matrix                            html  
    MA0004.1                                html  
    MotifSet-class                          html  
    PFMSimilarity-methods                   html  
    PWMSimilarity-methods                   html  
    SitePairSet-class                       html  
    SitePairSetList-class                   html  
    SiteSet-class                           html  
    SiteSetList-class                       html  
    TFBSTools-package                       html  
    TFFM-class                              html  
    XMatrix-class                           html  
    XMatrixList-class                       html  
    calConservation-methods                 html  
    deleteMatrixHavingID-methods            html  
    dmmEM-methods                           html  
    getEmissionProb                         html  
    getMatrixByID-methods                   html  
    getMatrixSet-methods                    html  
    getPosProb                              html  
    makeFlatFileDir                         html  
    permuteMatrix-methods                   html  
    rPWMDmm-methods                         html  
    readXMLTFFM                             html  
    runMEME-methods                         html  
    sampleRanges                            html  
    searchAln-methods                       html  
    searchPairBSgenome-methods              html  
    searchSeq-methods                       html  
    seqLogo                                 html  
    shannon.entropy                         html  
    toGRangesList-methods                   html  
    toICM-methods                           html  
    finding level-2 HTML links ... done

    toPWM-methods                           html  
Rd warning: /tmp/RtmpKoroP7/R.INSTALL7b8a300228bb/TFBSTools/man/toPWM-methods.Rd:91: missing file link 'PWM'
    writeGFF3-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TFBSTools)
Making 'packages.html' ... done