piano

Package: piano
Type: Package
Title: Platform for integrative analysis of omics data
Version: 1.12.0
Date: 2015-11-23
Author@R: c(person("Leif", "Varemo", email = "piano.rpkg@gmail.com",
role = "aut"), person("Intawat", "Nookaew", email =
"piano.rpkg@gmail.com", role = "aut"))
Author: Leif Varemo <piano.rpkg@gmail.com> and Intawat Nookaew <piano.rpkg@gmail.com>
Maintainer: Leif Varemo <piano.rpkg@gmail.com>
Depends: R (>= 2.14.0)
Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray
Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi
Description: Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.
License: GPL (>=2)
biocViews: Microarray, Preprocessing, QualityControl,
DifferentialExpression, Visualization, GeneExpression,
GeneSetEnrichment, Pathways
URL: http://www.sysbio.se/piano
NeedsCompilation: no
Packaged: 2016-05-05 03:50:40 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'piano' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
** help
*** installing help indices
  converting help for package 'piano'
    finding HTML links ... done
    GSAheatmap                              html  
    GSAsummaryTable                         html  
    consensusHeatmap                        html  
    consensusScores                         html  
    diffExp                                 html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/diffExp.Rd:67: missing file link 'limma'
Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/diffExp.Rd:119: missing file link 'limma'
    extractFactors                          html  
    geneSetSummary                          html  
    gsa_input                               html  
    gsa_results                             html  
    loadGSC                                 html  
    loadMAdata                              html  
Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/loadMAdata.Rd:116: missing file link 'yeast2.db'
    networkPlot                             html  
    piano-package                           html  
Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/piano-package.Rd:13: missing file link 'limma-package'
    polarPlot                               html  
    runGSA                                  html  
Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/runGSA.Rd:142: missing file link 'HTSanalyzeR-package'
Rd warning: /tmp/RtmpO7Th0s/R.INSTALL22062c1785e4/piano/man/runGSA.Rd:142: missing file link 'limma'
    runGSAhyper                             html  
    runQC                                   html  
    writeFilesForKiwi                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::union' by 'igraph::union' when loading 'piano'
Warning: replacing previous import 'BiocGenerics::normalize' by 'igraph::normalize' when loading 'piano'
* DONE (piano)
Making 'packages.html' ... done