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INSTALL report for openCyto on tokay2

This page was generated on 2018-10-17 08:37:50 -0400 (Wed, 17 Oct 2018).

Package 1030/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.18.0
Mike Jiang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/openCyto
Branch: RELEASE_3_7
Last Commit: a6b6850
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 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  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: openCyto
Version: 1.18.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/openCyto_1.18.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL openCyto_1.18.0.zip && rm openCyto_1.18.0.tar.gz openCyto_1.18.0.zip
StartedAt: 2018-10-16 19:47:57 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:50:13 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 135.8 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/openCyto_1.18.0.tar.gz && rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=openCyto.buildbin-libdir openCyto_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL openCyto_1.18.0.zip && rm openCyto_1.18.0.tar.gz openCyto_1.18.0.zip
###
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install for i386

* installing *source* package 'openCyto' ...
** libs
C:/Rtools/mingw_32/bin/g++  -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:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -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:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
misc.cpp: In function 'Rcpp::NumericMatrix collapseData(Rcpp::List, Rcpp::StringVector)':
misc.cpp:10:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i = 0; i < mat_list.size(); i++){
                        ^
misc.cpp:21:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned ind = 0; ind < mat_list.size(); ind++){
                               ^
C:/Rtools/mingw_32/bin/gcc  -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:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o misc.o unlockNamespace.o -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/openCyto.buildbin-libdir/openCyto/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'openCyto'
    finding HTML links ... done
    add                                     html  
    add_pop                                 html  
    as.data.table.gatingTemplate            html  
    boolMethod-class                        html  
    dims-gtMethod-method                    html  
    dummyMethod-class                       html  
    fcEllipsoidGate-class                   html  
    fcEllipsoidGate                         html  
    fcFilter-class                          html  
    fcFilterList-class                      html  
    fcFilterList                            html  
    fcPolygonGate-class                     html  
    fcPolygonGate                           html  
    fcRectangleGate-class                   html  
    fcRectangleGate                         html  
    fcTree-class                            html  
    fcTree                                  html  
    flowClust1d                             html  
    finding level-2 HTML links ... done

    flowClust2d                             html  
    gate_mindensity                         html  
    gate_mindensity2                        html  
    gate_quad_sequential                    html  
    gate_quad_tmix                          html  
    gate_quantile                           html  
    gate_tail                               html  
    gating-gtMethod-GatingSet-method        html  
    gating-methods                          html  
    gatingTemplate-class                    html  
    getChildren-gatingTemplate-character-method
                                            html  
    getGate-fcTree-character-method         html  
    getGate-gatingTemplate-character-method
                                            html  
    getNodes-fcTree-method                  html  
    getNodes                                html  
    getParent-gatingTemplate-character-method
                                            html  
    groupBy-gtMethod-method                 html  
    gtMethod-class                          html  
    gtPopulation-class                      html  
    gtSubsets-class                         html  
    isCollapse-gtMethod-method              html  
    isPolyfunctional                        html  
    listgtMethods                           html  
    names-gtMethod-method                   html  
    names-gtPopulation-method               html  
    ocRectRefGate-class                     html  
    ocRectRefGate                           html  
    ocRectangleGate-class                   html  
    openCyto                                html  
    openCyto.options                        html  
    parameters-gtMethod-method              html  
    plot-fcFilterList-ANY-method            html  
    plot-fcTree-character-method            html  
    plot-gatingTemplate-missing-method      html  
    polyFunctions-class                     html  
    posteriors-fcFilter-ANY-method          html  
    ppMethod-class                          html  
    ppMethod-gatingTemplate-character-method
                                            html  
    preprocessing-ppMethod-GatingSet-method
                                            html  
    prior_flowClust                         html  
    prior_flowClust1d                       html  
    prior_kmeans                            html  
    priors-fcFilter-ANY-method              html  
    refGate-class                           html  
    registerPlugins                         html  
    show-boolMethod-method                  html  
    show-fcFilter-method                    html  
    show-gatingTemplate-method              html  
    show-gtMethod-method                    html  
    templateGen                             html  
    toggle.helperGates                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'openCyto' ...
** libs
C:/Rtools/mingw_64/bin/g++  -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:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -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:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
C:/Rtools/mingw_64/bin/gcc  -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:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c unlockNamespace.c -o unlockNamespace.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o openCyto.dll tmp.def RcppExports.o misc.o unlockNamespace.o -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/openCyto.buildbin-libdir/openCyto/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'openCyto' as openCyto_1.18.0.zip
* DONE (openCyto)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'openCyto' successfully unpacked and MD5 sums checked
In R CMD INSTALL