Back to Multiple platform build/check report for BioC 3.7
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

BUILD BIN report for flowCore on tokay2

This page was generated on 2018-10-17 08:33:02 -0400 (Wed, 17 Oct 2018).

Package 502/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 1.46.2
M.Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowCore
Branch: RELEASE_3_7
Last Commit: d99c7f6
Last Changed Date: 2018-09-11 18:20:06 -0400 (Tue, 11 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCore
Version: 1.46.2
Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_1.46.2.tar.gz
StartedAt: 2018-10-17 06:19:58 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 06:22:20 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 142.3 seconds
RetCode: 0
Status:  OK  
PackageFile: flowCore_1.46.2.zip
PackageFileSize: 8.453 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_1.46.2.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCore'
    finding HTML links ... done
    EHtrans-class                           html  
    FCSTransTransform                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiFHFs/R.INSTALL28f04ac2902/flowCore/man/FCSTransTransform.Rd:42: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    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: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiFHFs/R.INSTALL28f04ac2902/flowCore/man/filters-class.Rd:13: file link 'filterList' in package 'flowCore' does not exist and so has been treated as a topic
    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: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiFHFs/R.INSTALL28f04ac2902/flowCore/man/logicleTransform.Rd:50: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    logicletGml2-class                      html  
    logtGml2-class                          html  
    manyFilterResult-class                  html  
    markernames                             html  
    multipleFilterResult-class              html  
    norm2Filter-class                       html  
    normalization-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiFHFs/R.INSTALL28f04ac2902/flowCore/man/normalization-class.Rd:82: file link 'normalize-methods' in package 'flowStats' does not exist and so has been treated as a topic
    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
In R CMD INSTALL

install for x64

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c biexponential.cpp -o biexponential.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c convertRawBytes.cpp -o convertRawBytes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c fcsTextParse.cpp -o fcsTextParse.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hyperlogTransform.cpp -o hyperlogTransform.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c logicleTransform.cpp -o logicleTransform.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c sortBytes.cpp -o sortBytes.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.46.2.zip
* DONE (flowCore)
In R CMD INSTALL
In R CMD INSTALL