* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘varitas’ ...
** package ‘varitas’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘varitas’
    finding HTML links ... done
    add.option                              html  
    alternate.gene.sort                     html  
    build.variant.specification             html  
    caller.overlap.venn.diagram             html  
    capitalize.caller                       html  
    classify.variant                        html  
    convert.ides.output                     html  
    create.directories                      html  
    date.stamp.file.name                    html  
    extract.sample.ids                      html  
    filter.variant.file                     html  
    filter.variants                         html  
    fix.lofreq.af                           html  
    fix.names                               html  
    fix.varscan.af                          html  
    get.base.substitution                   html  
    get.bed.chromosomes                     html  
    get.buildver                            html  
    get.colours                             html  
    get.coverage.by.amplicon                html  
    get.coverage.by.sample.statistics       html  
    get.fasta.chromosomes                   html  
    get.file.path                           html  
    get.filters                             html  
    get.gene                                html  
    get.miniseq.sample.files                html  
    get.option                              html  
    get.panel.coverage.by.gene              html  
    get.pool.from.panel.data                html  
    get.varitas.options                     html  
    get.vcf.chromosomes                     html  
    in.varitas.options                      html  
    logical.to.character                    html  
    make.command.line.call                  html  
    mean.field.value                        html  
    merge.ides.annotation                   html  
    merge.variants                          html  
    overwrite.varitas.options               html  
    parse.job.dependencies                  html  
    plot.amplicon.coverage.per.sample       html  
    plot.coverage.by.genome.order           html  
    plot.coverage.by.sample                 html  
    plot.ontarget.percent                   html  
    plot.paired.percent                     html  
    post.processing                         html  
    prepare.bam.specification               html  
    prepare.fastq.specification             html  
    prepare.miniseq.specifications          html  
    prepare.vcf.specification               html  
    process.coverage.reports                html  
    process.sample.contamination.checks     html  
    process.total.coverage.statistics       html  
    read.all.calls                          html  
    read.ides.file                          html  
    read.variant.calls                      html  
    read.yaml                               html  
    run.alignment                           html  
    run.alignment.sample                    html  
    run.all.scripts                         html  
    run.annotation                          html  
    run.annovar.vcf                         html  
    run.filtering.txt                       html  
    run.ides                                html  
    run.lofreq.sample                       html  
    run.muse.sample                         html  
    run.mutect.sample                       html  
    run.post.processing                     html  
    run.target.qc                           html  
    run.target.qc.sample                    html  
    run.vardict.sample                      html  
    run.variant.calling                     html  
    run.varitas.pipeline                    html  
    run.varitas.pipeline.hybrid             html  
    run.varscan.sample                      html  
    save.config                             html  
    save.coverage.excel                     html  
    save.variants.excel                     html  
    set.varitas.options                     html  
    split.on.column                         html  
    sum.dp4                                 html  
    system.ls                               html  
    tabular.mean                            html  
    tabular.median                          html  
    trinucleotide.barplot                   html  
    variant.recurrence.barplot              html  
    variants.caller.barplot                 html  
    variants.sample.barplot                 html  
    verify.bam.specification                html  
    verify.bwa.index                        html  
    verify.fasta.index                      html  
    verify.fastq.specification              html  
    verify.sequence.dictionary              html  
    verify.varitas.options                  html  
    verify.vcf.specification                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (varitas)