Last data update: 2014.03.03


Package: Pbase
Type: Package
Title: Manipulating and exploring protein and proteomics data
Version: 0.12.2
Authors@R: c(person("Laurent", "Gatto", role = c("aut", "cre"),
email = ""),
person("Sebastian", "Gibb", role = c("aut", "cre"),
email = ""))
Depends: R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz
Imports: cleaver (>= 1.3.6), Biobase, Biostrings, IRanges, S4Vectors,
mzID, mzR (>= 1.99.1), MSnbase (>= 1.15.5), Pviz, biomaRt,
GenomicRanges, rtracklayer
Suggests: testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr,
rmarkdown, BiocStyle
Description: A set of classes and functions to investigate and
understand protein sequence data in the context of a
proteomics experiment.
License: GPL-3
Author: Laurent Gatto [aut], Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <>,
Laurent Gatto <>
VignetteBuilder: knitr
biocViews: Infrastructure, Proteomics, MassSpectrometry, Visualization,
DataImport, DataRepresentation
NeedsCompilation: no
Packaged: 2016-05-16 04:38:25 UTC; biocbuild

● BiocViews: DataImport, DataRepresentation, Infrastructure, MassSpectrometry, Proteomics, Visualization
6 images, 8 functions, 1 datasets
● Reverse Depends: 0

Install log

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

Rd warning: /tmp/RtmpTcFGbV/R.INSTALL1526207fed0/Pbase/man/Proteins-class.Rd:202: missing file link 'cleave'
    calculateHeavyLabels                    html  
    coordinate-mapping-methods              html  
Rd warning: /tmp/RtmpTcFGbV/R.INSTALL1526207fed0/Pbase/man/coordinate-mapping-methods.Rd:86: missing file link 'mapToAlignments'
Rd warning: /tmp/RtmpTcFGbV/R.INSTALL1526207fed0/Pbase/man/coordinate-mapping-methods.Rd:91: missing file link 'mapToTranscripts'
    etrid2grl                               html  
    isReverse                               html  
    p                                       html  
    plotAsAnnotationTrack                   html  
    proteinCoding-methods                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Pbase)
Making 'packages.html' ... done