openCyto

Package: openCyto
Type: Package
Title: Hierarchical Gating Pipeline for flow cytometry data
Version: 1.10.3
Date: 2012-06-11
Author: Mike Jiang, John Ramey, Greg Finak, Raphael Gottardo
Maintainer: Mike Jiang <wjiang2@fhcrc.org>
Description: This package is designed to facilitate the automated gating
methods in sequential way to mimic the manual gating strategy.
License: Artistic-2.0
LazyLoad: yes
Depends: flowWorkspace (>= 3.17.43)
Imports: methods, Biobase, gtools, flowCore (>=
1.31.17), flowViz, ncdfFlow (>=
2.11.34), flowWorkspace, flowStats (>=
3.29.1), flowClust, MASS, clue, plyr, RBGL, graph, data.table, ks, RColorBrewer, lattice, rrcov, R.utils
Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel
biocViews: FlowCytometry, DataImport, Preprocessing, DataRepresentation
VignetteBuilder: knitr
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2016-05-16 04:09:01 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'openCyto' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c misc.cpp -o misc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c unlockNamespace.c -o unlockNamespace.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o openCyto.so RcppExports.o misc.o unlockNamespace.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/openCyto/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'openCyto'
    finding HTML links ... done
    add                                     html  
    add_pop                                 html  
    as.data.table.gatingTemplate            html  
    boolMethod-class                        html  
    dims-gtMethod-method                    html  
    dummyMethod-class                       html  
    fcEllipsoidGate-class                   html  
    fcEllipsoidGate                         html  
    fcFilter-class                          html  
    fcFilterList-class                      html  
    fcFilterList                            html  
    fcPolygonGate-class                     html  
    fcPolygonGate                           html  
    fcRectangleGate-class                   html  
    fcRectangleGate                         html  
    fcTree-class                            html  
    fcTree                                  html  
    filterObject-logicalFilterResult-method
                                            html  
    flowClust1d                             html  
    finding level-2 HTML links ... done

    flowClust2d                             html  
    gating-boolMethod-GatingSet-method      html  
    gating-gtMethod-GatingSet-method        html  
    gating-methods                          html  
    gating-polyFunctions-GatingSet-method   html  
    gating-refGate-GatingSet-method         html  
    gatingTemplate-class                    html  
    getChildren-gatingTemplate-character-method
                                            html  
    getGate-fcTree-character-method         html  
    getGate-gatingTemplate-character-method
                                            html  
    getNodes-fcTree-method                  html  
    getNodes                                html  
    getParent-gatingTemplate-character-method
                                            html  
    groupBy-gtMethod-method                 html  
    gtMethod-class                          html  
    gtPopulation-class                      html  
    gtSubsets-class                         html  
    isCollapse-gtMethod-method              html  
    isPolyfunctional                        html  
    listgtMethods                           html  
    mindensity                              html  
    mindensity2                             html  
    names-gtMethod-method                   html  
    names-gtPopulation-method               html  
    ocRectRefGate-class                     html  
    ocRectRefGate                           html  
    ocRectangleGate-class                   html  
    openCyto                                html  
    parameters-gtMethod-method              html  
    plot-fcFilterList-ANY-method            html  
    plot-fcTree-character-method            html  
    plot-gatingTemplate-missing-method      html  
    polyFunctions-class                     html  
    posteriors-fcFilter-ANY-method          html  
    ppMethod-class                          html  
    ppMethod-gatingTemplate-character-method
                                            html  
    preprocessing-ppMethod-GatingSet-method
                                            html  
    prior_flowClust                         html  
    prior_flowClust1d                       html  
    prior_kmeans                            html  
    priors-fcFilter-ANY-method              html  
    quadGate.seq                            html  
    quadGate.tmix                           html  
    quantileGate                            html  
    refGate-class                           html  
    registerPlugins                         html  
    show-boolMethod-method                  html  
    show-fcFilter-method                    html  
    show-gatingTemplate-method              html  
    show-gtMethod-method                    html  
    tailgate                                html  
    templateGen                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (openCyto)
Making 'packages.html' ... done