GGtools

Package: GGtools
Title: software and data for analyses in genetics of gene expression
Version: 5.8.0
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: software and data for analyses in genetics of gene expression
and/or DNA methylation
Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel,
Homo.sapiens
Imports: methods, utils, stats, BiocGenerics, snpStats, ff, Rsamtools,
AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin,
rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges, iterators, Biostrings, ROCR,
biglm, ggplot2, reshape2
Enhances: MatrixEQTL, foreach, doParallel, gwascat
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
biocViews: Genetics, GeneExpression, GeneticVariability, SNP
LazyLoad: yes
Packaged: 2016-05-04 02:57:50 UTC; biocbuild
Collate: AllClasses.R AllGenerics.R eqtlTests.R managers.R topFeats.R
gwSnpTests.R snpsCisToGenes.R relocate.R topSnps.R
snplocsDefault.R transutils.R vcfutils.R eqtlEstimates.R
alleq.R meta.R eqME.R meta.all.R best.trans.eQTLs.R
meta.transScores.R summInfra.R bindmaf.R fdr.all.cis.R pifdr.R
getFDR.R cisConfig.R thinclass.R harvest.R scoredist.R binqq.R
gffprocess.R cisEqTools.R modutils.R seqinfo.R pureSensSoft.R
cisa.R scan.R basicappraise.R Eqappr.R
NeedsCompilation: no

Install log

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

Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/CisConfig-class.Rd:115: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/CisConfig-class.Rd:173: missing file link 'Matrix_eQTL_engine'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/CisConfig-class.Rd:178: missing file link 'Matrix_eQTL_engine'
    EqAppr-class                            html  
    GGtools-package                         html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/GGtools-package.Rd:68: missing file link 'getSS'
    TransConfig-class                       html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/TransConfig-class.Rd:42: missing file link 'getSS'
    appraise                                html  
    b1                                      html  
    best.cis.eQTLs                          html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.cis.eQTLs.Rd:95: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.cis.eQTLs.Rd:136: missing file link 'snplocs'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.cis.eQTLs.Rd:196: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.cis.eQTLs.Rd:200: missing file link 'getSS'
    best.trans.eQTLs                        html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.trans.eQTLs.Rd:21: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.trans.eQTLs.Rd:41: missing file link 'ffrowapply'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/best.trans.eQTLs.Rd:65: missing file link 'snplocs'
    bindmaf                                 html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/bindmaf.Rd:24: missing file link 'getSS'
    cgff2dt                                 html  
    cisAssoc                                html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/cisAssoc.Rd:26: missing file link 'TabixFile'
    cisRun-class                            html  
    ciseqByCluster                          html  
    collectBest                             html  
    concatCis                               html  
    eqBox                                   html  
    eqsens_dt                               html  
    eqtlTests                               html  
    eqtlTests.me                            html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/eqtlTests.me.Rd:45: missing file link 'Matrix_eQTL_engine'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/eqtlTests.me.Rd:71: missing file link 'Matrix_eQTL_engine'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/eqtlTests.me.Rd:84: missing file link 'regressOut'
    eqtlTestsManager-class                  html  
    ex                                      html  
    getCisMap                               html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/getCisMap.Rd:31: missing file link 'snplocs'
    gffprocess                              html  
    gwSnpTests                              html  
    hmm878                                  html  
    pifdr                                   html  
    qqhex                                   html  
    richNull                                html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/richNull.Rd:33: missing file link 'getSS'
    sampsInVCF                              html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/sampsInVCF.Rd:17: missing file link 'TabixFile'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/sampsInVCF.Rd:39: missing file link 'TabixFile'
    scoresCis                               html  
    sensanal                                html  
    sensiCisInput-class                     html  
    sensiCisOutput-class                    html  
    simpleTiling                            html  
    snplocsDefault                          html  
    strMultPop                              html  
    transManager-class                      html  
    transScores                             html  
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/transScores.Rd:85: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/transScores.Rd:88: missing file link 'getSS'
Rd warning: /tmp/RtmpvwTonV/R.INSTALL54dd7c90ca4c/GGtools/man/transScores.Rd:91: missing file link 'ffrowapply'
    transTab                                html  
    transeqByCluster                        html  
    vcf2sm                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GGtools)
Making 'packages.html' ... done