gQTLstats

Package: gQTLstats
Title: gQTLstats: computationally efficient analysis for eQTL and
allied studies
Version: 1.4.2
Author: VJ Carey <stvjc@channing.harvard.edu>
Description: computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
Suggests: geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio,
BiocStyle, Homo.sapiens, RUnit, multtest
Depends: R (>= 3.1.0)
Imports: methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges,
SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs,
gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures,
ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc,
beeswarm
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
BiocViews: SNP, GenomeAnnotation, Genetics
NeedsCompilation: no
Packaged: 2016-05-16 05:09:42 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gQTLstats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gQTLstats'
    finding HTML links ... done
    FDRsupp-class                           html  
    TransStore-class                        html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/TransStore-class.Rd:19: missing file link 'Registry'
    TransStore                              html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/TransStore.Rd:16: missing file link 'Registry'
    cisAssoc                                html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/cisAssoc.Rd:34: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/cisAssoc.Rd:37: missing file link 'TabixFile'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/cisAssoc.Rd:60: missing file link 'col.summary'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/cisAssoc.Rd:72: missing file link 'isSNV'
    clipPCs                                 html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/clipPCs.Rd:24: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/clipPCs.Rd:50: missing file link 'RangedSummarizedExperiment'
    directPlot                              html  
    enumerateByFDR                          html  
    finding level-2 HTML links ... done

    eqBox2                                  html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/eqBox2.Rd:24: missing file link 'RangedSummarizedExperiment'
    filtFDR                                 html  
    gQTLs                                   html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/gQTLs.Rd:29: missing file link 'readVcf'
    gQTLstats-package                       html  
    hmm878                                  html  
    manhWngr                                html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/manhWngr.Rd:28: missing file link 'GRanges'
    mixedVCFtoSnpMatrix                     html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:18: missing file link 'CollapsedVCF-class'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:24: missing file link 'genotypeToSnpMatrix'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:32: missing file link 'genotypeToSnpMatrix'
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/mixedVCFtoSnpMatrix.Rd:50: missing file link 'genotypeToSnpMatrix'
    pifdr                                   html  
    qqStore                                 html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/qqStore.Rd:28: missing file link 'storeToQuantiles'
    queryVCF                                html  
Rd warning: /tmp/RtmprCq6EO/R.INSTALL2dfe4cd635e2/gQTLstats/man/queryVCF.Rd:29: missing file link 'genotypeToSnpMatrix'
    senstab                                 html  
    setFDRfunc                              html  
    storeToStats                            html  
    transAssoc                              html  
    txsPlot                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gQTLstats)
Making 'packages.html' ... done