VariantTools

Package: VariantTools
Type: Package
Title: Tools for Working with Genetic Variants
Version: 1.14.1
Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Maintainer: Michael Lawrence <michafla@gene.com>
Description: Tools for detecting, filtering, calling, comparing and
plotting variants.
Depends: S4Vectors (>= 0.9.25), IRanges (>= 1.99.2), GenomicRanges (>=
1.17.7), VariantAnnotation (>= 1.11.16), methods
Imports: Rsamtools (>= 1.17.6), BiocGenerics, Biostrings, parallel,
gmapR (>= 1.13.4), GenomicFeatures (>= 1.17.13), Matrix,
rtracklayer (>= 1.25.3), BiocParallel, GenomeInfoDb, BSgenome,
Biobase
Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph
License: Artistic-2.0
LazyLoad: yes
biocViews: Genetics, GeneticVariability, Sequencing
NeedsCompilation: no
Packaged: 2016-05-20 03:38:31 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'VariantTools' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'VariantTools'
    finding HTML links ... done
    FilterConstructors                      html  
    annnotateWithControlDepth               html  
    callGenotypes                           html  
    callSampleSpecificVariants              html  
    callVariants                            html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/callVariants.Rd:82: missing file link 'bam_tally'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/callVariants.Rd:84: missing file link 'FilterRules'
    callWildtype                            html  
    concordance                             html  
    extractCoverageForPositions             html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/extractCoverageForPositions.Rd:16: missing file link 'coverage'
    matchVariants                           html  
    pileupVariants                          html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/pileupVariants.Rd:11: missing file link 'bam_tally'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/pileupVariants.Rd:21: missing file link 'PileupFiles'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/pileupVariants.Rd:28: missing file link 'ApplyPileupsParam'
    postFilterVariants                      html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/postFilterVariants.Rd:50: missing file link 'FilterRules'
    qaVariants                              html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/qaVariants.Rd:51: missing file link 'FilterRules'
    tallyVariants                           html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/tallyVariants.Rd:46: missing file link 'stackSamples'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/tallyVariants.Rd:51: missing file link 'BamTallyParam'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/tallyVariants.Rd:58: missing file link 'BamTallyParam'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/tallyVariants.Rd:60: missing file link 'GmapGenome'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/tallyVariants.Rd:78: missing file link 'gsnap'
    variantGR2Vcf                           html  
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/variantGR2Vcf.Rd:8: missing file link 'VCF'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/variantGR2Vcf.Rd:10: missing file link 'writeVcf'
Rd warning: /tmp/RtmpoejMfI/R.INSTALL10cf2f5ffdba/VariantTools/man/variantGR2Vcf.Rd:19: missing file link 'VRanges'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantTools)
Making 'packages.html' ... done