Last data update: 2014.03.03

flowCore

Package: flowCore
Title: flowCore: Basic structures for flow cytometry data
Version: 1.38.2
Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan, J.
Spidlen, M. Jiang
Description: Provides S4 data structures and basic functions to deal with flow
cytometry data.
Maintainer: M.Jiang <wjiang2@fhcrc.org>
Depends: R (>= 2.10.0)
Imports: Biobase, BiocGenerics (>= 0.1.14), graph, graphics, methods,
rrcov, stats, utils, stats4, corpcor, Rcpp, matrixStats
Suggests: Rgraphviz, flowViz, flowStats, testthat,
flowWorkspace, flowWorkspaceData, openCyto
Collate: AllGenerics.R AllClasses.R flowFrame-accessors.R
flowSet-accessors.R Rm-methods.R actionItem-accessors.R
coerce.R logicalFilterResult-accessors.R
summarizeFilter-methods.R filterSummary-accessors.R
fcReference-accessors.R manyFilterResult-accessors.R
summary-methods.R multipleFilterResult-accessors.R on-methods.R
transformList-accessors.R identifier-methods.R
parameters-methods.R view-accessors.R initialize-methods.R
filterResult-accessors.R in-methods.R rectangleGate-accessors.R
workFlow-accessors.R filterResultList-accessors.R IO.R
show-methods.R length-methods.R names-methods.R
filterSet-accessors.R split-methods.R eval-methods.R gatingML.R
FCSTransTransform.R median-logicle-transform.R utils.R
RcppExports.R
License: Artistic-2.0
biocViews: Infrastructure, FlowCytometry, CellBasedAssays
LinkingTo: Rcpp, BH(>= 1.60.0-1)
SystemRequirements: GNU make
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-22 01:44:24 UTC; biocbuild

● BiocViews: CellBasedAssays, FlowCytometry, Infrastructure
● 9 images, 115 functions, 1 datasets
● Reverse Depends: 20

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'flowCore' ...
** libs
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c FastLogicle.cpp -o FastLogicle.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c Hyperlog.cpp -o Hyperlog.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c Logicle.cpp -o Logicle.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c biexponential.cpp -o biexponential.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c inPolygon.cpp -o inPolygon.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c inPolytope.cpp -o inPolytope.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c logicleTransform.cpp -o logicleTransform.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c uint2double.cpp -o uint2double.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c zeroin.cpp -o zeroin.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG -I../inst/include/  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/BH/include"   -fpic  -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
mkdir -p "/home/ddbj/local/lib64/R/library/flowCore/lib"
ar rs "/home/ddbj/local/lib64/R/library/flowCore/lib/libboost_regex.a" boost_regex/regex_traits_defaults.o boost_regex/usinstances.o boost_regex/fileiter.o boost_regex/static_mutex.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/posix_api.o boost_regex/wide_posix_api.o boost_regex/winstances.o boost_regex/cpp_regex_traits.o boost_regex/w32_regex_traits.o boost_regex/instances.o boost_regex/cregex.o boost_regex/c_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/icu.o boost_regex/regex_raw_buffer.o
ar: creating /home/ddbj/local/lib64/R/library/flowCore/lib/libboost_regex.a
g++ -std=c++11 -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o uint2double.o zeroin.o /home/ddbj/local/lib64/R/library/flowCore/lib/libboost_regex.a -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCore'
    finding HTML links ... done
    EHtrans-class                           html  
    FCSTransTransform                       html  
Rd warning: /tmp/RtmpREjw5I/R.INSTALL49f54e2acd8b/flowCore/man/FCSTransTransform.Rd:42: missing file link 'estimateLogicle'
    GvHD                                    html  
    Subset-methods                          html  
    actionItem-class                        html  
    arcsinhTransform                        html  
    asinht-class                            html  
    asinhtGml2-class                        html  
    biexponentialTransform                  html  
    boundaryFilter-class                    html  
    characterOrTransformation-class         html  
    checkOffset                             html  
    coerce                                  html  
    compensateActionItem-class              html  
    compensateView-class                    html  
    compensatedParameter-class              html  
    compensation-class                      html  
    concreteFilter-class                    html  
    dg1polynomial-class                     html  
    each_col-methods                        html  
    ellipsoidGate                           html  
    estimateMedianLogicle                   html  
    exponential-class                       html  
    expressionFilter-class                  html  
    fcReference-class                       html  
    filter-and-methods                      html  
    filter-class                            html  
    filter-in-methods                       html  
    filter-methods                          html  
    filter-on-methods                       html  
    filterDetails-methods                   html  
    filterList-class                        html  
    filterReference-class                   html  
    filterResult-class                      html  
    filterResultList-class                  html  
    filterSet-class                         html  
    filterSummary-class                     html  
    filterSummaryList-class                 html  
    filters-class                           html  
Rd warning: /tmp/RtmpREjw5I/R.INSTALL49f54e2acd8b/flowCore/man/filters-class.Rd:13: missing file link 'filterList'
    flowCore-package                        html  
    flowFrame-class                         html  
    flowSet-class                           html  
    fsApply                                 html  
    gateActionItem-class                    html  
    gateView-class                          html  
    getChannelMarker                        html  
    getIndexSort-methods                    html  
    hyperlog-class                          html  
    hyperlogtGml2-class                     html  
    identifier-methods                      html  
    inverseLogicleTransform                 html  
    invsplitscale-class                     html  
    keyword-methods                         html  
    kmeansFilter                            html  
    linearTransform                         html  
    lintGml2-class                          html  
    lnTransform                             html  
    logTransform                            html  
    logarithm-class                         html  
    logicalFilterResult-class               html  
    logicleTransform                        html  
Rd warning: /tmp/RtmpREjw5I/R.INSTALL49f54e2acd8b/flowCore/man/logicleTransform.Rd:50: missing file link 'estimateLogicle'
    logicletGml2-class                      html  
    logtGml2-class                          html  
    manyFilterResult-class                  html  
    markernames                             html  
    multipleFilterResult-class              html  
    norm2Filter-class                       html  
    normalization-class                     html  
Rd warning: /tmp/RtmpREjw5I/R.INSTALL49f54e2acd8b/flowCore/man/normalization-class.Rd:82: missing file link 'normalize-methods'
    normalizeActionItem-class               html  
    normalizeView-class                     html  
    parameterFilter-class                   html  
    parameterTransform-class                html  
    parameters-class                        html  
    parameters-methods                      html  
    polygonGate                             html  
    polytopeGate                            html  
    quadGate                                html  
    quadratic-class                         html  
    quadraticTransform                      html  
    randomFilterResult-class                html  
    ratio-class                             html  
    ratiotGml2-class                        html  
    read.FCS                                html  
    read.FCSheader                          html  
    read.flowSet                            html  
    rectangleGate                           html  
    sampleFilter-class                      html  
    scaleTransform                          html  
    setOperationFilter-class                html  
    singleParameterTransform-class          html  
    sinht-class                             html  
    spillover-flowSet                       html  
    split-methods                           html  
    splitScaleTransform                     html  
    splitscale-class                        html  
    squareroot-class                        html  
    subsetting-class                        html  
    subsettingActionItem-class              html  
    subsettingView-class                    html  
    summarizeFilter-methods                 html  
    timeFilter-class                        html  
    transform-class                         html  
    transformActionItem-class               html  
    transformFilter-class                   html  
    transformList-class                     html  
    transformMap-class                      html  
    transformReference-class                html  
    transformView-class                     html  
    transformation-class                    html  
    truncateTransform                       html  
    unitytransform-class                    html  
    validFilters                            html  
    view-class                              html  
    workFlow-class                          html  
    write.FCS                               html  
    write.flowSet                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO