GGBase

Package: GGBase
Title: infrastructure for genetics of gene expression (c) 2008 VJ Carey
Version: 3.16.0
Author: Vince Carey <stvjc@channing.harvard.edu>
Description: infrastructure for dealing with hapmap SNP reports, GWAS, etc.
Depends: R (>= 2.13.0), methods, BiocGenerics, Biobase (>= 2.13.0),
snpStats(>= 1.1.10), RSQLite, genefilter
Imports: methods, BiocGenerics, AnnotationDbi
Suggests: illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20090506
LazyLoad: yes
biocViews: SNP, GeneticVariability, Genetics, Bioinformatics
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
License: Artistic-2.0
Collate: AllClasses.R testOutputClasses.R snpLocs.Hsapiens.R
ScreenResult-methods.R snpLocs-methods.R smlSet-methods.R snpsNear.R
pedinf2df.R isCis.R snpFilters.R featureFilter.R make_smlSet.R zzz.R

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GGBase' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GGBase'
    finding HTML links ... done
    MAFfilter                               html  
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/MAFfilter.Rd:37: missing file link 'col.summary'
    clipPCs                                 html  
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/clipPCs.Rd:27: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/clipPCs.Rd:31: missing file link 'RangedSummarizedExperiment'
    externalize                             html  
    make_smlSet                             html  
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/make_smlSet.Rd:22: missing file link 'ExpressionSet-class'
    plot_EvG                                html  
    rsid-class                              html  
    finding level-2 HTML links ... done

    smlSet-class                            html  
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/smlSet-class.Rd:35: missing file link 'AssayData-class'
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/smlSet-class.Rd:37: missing file link 'AnnotatedDataFrame-class'
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/smlSet-class.Rd:41: missing file link 'MIAxE-class'
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/smlSet-class.Rd:44: missing file link 'eSet-class'
Rd warning: /tmp/RtmpSnF0fA/R.INSTALL549047a8ab34/GGBase/man/smlSet-class.Rd:65: missing file link 'nsFilter,ExpressionSet-method'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GGBase)
Making 'packages.html' ... done