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INSTALL report for flowWorkspace on tokay2

This page was generated on 2019-04-09 11:59:19 -0400 (Tue, 09 Apr 2019).

Package 577/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.31.15
Greg Finak ,Mike Jiang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: master
Last Commit: 6803ddb
Last Changed Date: 2019-04-08 14:02:14 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK YES, new version is higher than in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: flowWorkspace
Version: 3.31.15
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowWorkspace_3.31.15.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.31.15.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.31.15.zip && rm flowWorkspace_3.31.15.tar.gz flowWorkspace_3.31.15.zip
StartedAt: 2019-04-08 19:31:56 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 19:39:52 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 476.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/flowWorkspace_3.31.15.tar.gz && rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowWorkspace.buildbin-libdir flowWorkspace_3.31.15.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.31.15.zip && rm flowWorkspace_3.31.15.tar.gz flowWorkspace_3.31.15.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2634k  100 2634k    0     0  29.9M      0 --:--:-- --:--:-- --:--:-- 32.5M

install for i386

* installing *source* package 'flowWorkspace' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/lib/i386/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/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 getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/i386/libprotobuf.a -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/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  
    GatingSetList-class                     html  
    add                                     html  
    asinh_Gml2                              html  
    asinhtGml2_trans                        html  
    booleanFilter-class                     html  
    finding level-2 HTML links ... done

    checkRedundantNodes                     html  
    clone                                   html  
    compensate                              html  
    compute_timestep                        html  
    copyNode                                html  
    dropRedundantChannels                   html  
    dropRedundantNodes                      html  
    estimateLogicle.GatingHierarchy         html  
    extract_cluster_pop_name_from_node      html  
    filterObject                            html  
    fix_channel_slash                       html  
    flowData                                html  
    flowJo.fasinh                           html  
    flowJo.flog                             html  
    flowJoTrans                             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  
    getCompensationObj                      html  
    getData-methods                         html  
    getDescendants                          html  
    getFullNodePath                         html  
    getGate                                 html  
    getIndiceMat                            html  
    getIndices-GatingSet-name-method        html  
    getIndices                              html  
    getMergedStats                          html  
    getNodes                                html  
    getParent                               html  
    getPopStats                             html  
    getSingleCellExpression                 html  
    getStats                                html  
    getTransformations                      html  
    get_leaf_nodes                          html  
    gh_check_cluster_node                   html  
    gh_get_cluster_labels                   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  
    nodeflags                               html  
    openWorkspace                           html  
    pData-methods                           html  
    plot-methods                            html  
    plotGate-methods                        html  
    plotPopCV                               html  
    plot_diff_tree                          html  
    prettyAxis                              html  
    recompute                               html  
    rotate_gate                             html  
    sampleNames                             html  
    save_gs                                 html  
    scale_gate                              html  
    set.count.xml                           html  
    setGate                                 html  
    setNode-methods                         html  
    shift_gate                              html  
    standardize-GatingSet                   html  
    stats.fun                               html  
    subset                                  html  
    swap_data_cols                          html  
    transform                               html  
    transform_gate                          html  
    transformerList                         html  
    updateChannels                          html  
    updateIndices-GatingHierarchy-character-logical-method
                                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flowWorkspace' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_API.cpp:9:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/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-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from R_GatingHierarchy.cpp:17:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_GatingSet.cpp -o R_GatingSet.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from R_GatingSet.cpp:10:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getDescendants.cpp -o getDescendants.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getDescendants.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getPopStats.cpp -o getPopStats.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from getPopStats.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from getSingleCellExpression.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -DROUT -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c setCounts.cpp -o setCounts.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:11,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:15,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:12,
                 from setCounts.cpp:1:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> BOOLINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function 'virtual std::vector<unsigned int> ROOTINDICES::getIndices_u()':
C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o getDescendants.o getPopStats.o getSingleCellExpression.o setCounts.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.9-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 getPopStats.o getSingleCellExpression.o setCounts.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/lib/x64/libprotobuf.a -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lws2_32 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.31.15.zip
* DONE (flowWorkspace)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked