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INSTALL report for CytoML on tokay2

This page was generated on 2019-10-16 12:36:11 -0400 (Wed, 16 Oct 2019).

Package 383/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CytoML 1.10.0
Mike Jiang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CytoML
Branch: RELEASE_3_9
Last Commit: b247ba4
Last Changed Date: 2019-05-02 11:54:02 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CytoML
Version: 1.10.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CytoML_1.10.0.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CytoML_1.10.0.zip && rm CytoML_1.10.0.tar.gz CytoML_1.10.0.zip
StartedAt: 2019-10-15 20:42:47 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:45:14 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 147.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CytoML_1.10.0.tar.gz && rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CytoML.buildbin-libdir CytoML_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CytoML_1.10.0.zip && rm CytoML_1.10.0.tar.gz CytoML_1.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 6140k  100 6140k    0     0  51.4M      0 --:--:-- --:--:-- --:--:-- 55.0M

install for i386

* installing *source* package 'CytoML' ...
** using staged installation

   **********************************************
   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-3~1.9-B/R/include" -DNDEBUG -DROUT -I../inst/include/ -Ic:/libxml2//i386/include/libxml2 -DLIBXML_STATIC -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 ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
                 from ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../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-3.9-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 ../inst/include/CytoML.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 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 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++)
                     ^
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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector&, std::vector&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i 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 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++)
                     ^
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 parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector&, std::vector&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i 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 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++)
                     ^
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 ../inst/include/CytoML.h:5,
                 from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector&, std::vector&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i 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 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++)
                     ^
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 parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function 'void workspace::toArray(std::string, std::vector&, std::vector&)':
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(unsigned i=0;i