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INSTALL report for flowWorkspace on tokay2

This page was generated on 2018-10-17 08:35:24 -0400 (Wed, 17 Oct 2018).

Package 525/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.28.2
Greg Finak ,Mike Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_7
Last Commit: bd5ee4c
Last Changed Date: 2018-09-12 18:32:05 -0400 (Wed, 12 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: flowWorkspace
Version: 3.28.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowWorkspace_3.28.2.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.28.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.28.2.zip && rm flowWorkspace_3.28.2.tar.gz flowWorkspace_3.28.2.zip
StartedAt: 2018-10-16 19:36:35 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:46:35 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 600.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowWorkspace_3.28.2.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.28.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.28.2.zip && rm flowWorkspace_3.28.2.tar.gz flowWorkspace_3.28.2.zip
###
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##############################################################################


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100 2825k  100 2825k    0     0  24.3M      0 --:--:-- --:--:-- --:--:-- 25.7M

install for i386

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                       ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:779:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:1291:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned j = 0; j < pops.size(); ++j){
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o c:/libxml2//i386/lib/libxml2.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowWorkspace'
    finding HTML links ... done
    GatingHierarchy-class                   html  
    GatingSet-class                         html  
    GatingSet-methods                       html  
    finding level-2 HTML links ... done

    GatingSetList-class                     html  
    add                                     html  
    asinh_Gml2                              html  
    asinhtGml2_trans                        html  
    booleanFilter-class                     html  
    checkRedundantNodes                     html  
    clone                                   html  
    compensate                              html  
    dropRedundantChannels                   html  
    dropRedundantNodes                      html  
    estimateLogicle.GatingHierarchy         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpeKdHJV/R.INSTALLf101cdf7f8a/flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd:20: file link 'estimateLogicle' in package 'flowCore' does not exist and so has been treated as a topic
    filterObject                            html  
    flowData                                html  
    flowJo.fasinh                           html  
    flowJo.flog                             html  
    flowJoTrans                             html  
    flowJoWorkspace-class                   html  
    flowJo_biexp_trans                      html  
    flowJo_fasinh_trans                     html  
    flowWorkspace-package                   html  
    flowWorkspace.par.get                   html  
    flowWorkspace.par.init                  html  
    flow_breaks                             html  
    flow_trans                              html  
    getCompensationMatrices                 html  
    getData-methods                         html  
    getDescendants                          html  
    getFJWSubsetIndices                     html  
    getGate                                 html  
    getIndiceMat                            html  
    getIndices-GatingSet-name-method        html  
    getIndices                              html  
    getKeywords                             html  
    getMergedStats                          html  
    getNodes                                html  
    getParent                               html  
    getPopStats                             html  
    getSampleGroups                         html  
    getSamples                              html  
    getSingleCellExpression                 html  
    getStats                                html  
    getTransformations                      html  
    groupByChannels                         html  
    groupByTree                             html  
    insertGate                              html  
    isNcdf                                  html  
    keyword                                 html  
    lapply-methods                          html  
    length                                  html  
    logicleGml2_trans                       html  
    logicle_trans                           html  
    loglevel                                html  
    logtGml2_trans                          html  
    markernames                             html  
    mkformula                               html  
    moveNode                                html  
    ncFlowSet-methods                       html  
    openWorkspace                           html  
    pData-methods                           html  
    parseWorkspace                          html  
    plot-methods                            html  
    plotGate-methods                        html  
    plotPopCV                               html  
    prettyAxis                              html  
    recompute                               html  
    sampleNames                             html  
    save_gs                                 html  
    set.count.xml                           html  
    setGate                                 html  
    setNode-methods                         html  
    standardize-GatingSet                   html  
    stats.fun                               html  
    subset                                  html  
    transform                               html  
    transformerList                         html  
    updateChannels                          html  
    updateIndices-GatingHierarchy-character-logical-method
                                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowWorkspace' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_API.cpp -o R_API.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
     * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
 ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector<double>&, std::vector<double>&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i<nLen;i++)
                       ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp: In member function 'virtual trans_local xFlowJoWorkspace::getTransformation(wsRootNode, const compensation&, PARAM_VEC&, trans_global_vec*, biexpTrans*, linTrans*, bool)':
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:779:12: warning: unused variable 'minRange' [-Wunused-variable]
     double minRange=atof(transNode.getProperty("minRange").c_str());
            ^
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
                 from ../inst/include/flowWorkspace/wsNode.hpp:10,
                 from ../inst/include/flowWorkspace/workspace.hpp:14,
                 from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
                 from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
                 from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/gate.hpp:1291:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),interpolated(false),quadrant(_quad){
                                                                                              ^
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from R_GatingSet.cpp:10:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:10: note: 'quad' was declared here
     QUAD quad;
          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//x64/include/libxml2 -DLIBXML_STATIC -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:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:2:
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < x.size(); i++){
                     ^
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.7-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nEvents; i++)
                     ^
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getSingleCellExpression.o setCounts.o c:/libxml2//x64/lib/libxml2.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.28.2.zip
* DONE (flowWorkspace)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
In R CMD INSTALL