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INSTALL report for flowWorkspace on malbec1

This page was generated on 2021-05-06 12:27:36 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowWorkspace package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 641/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 4.2.0  (landing page)
Greg Finak ,Mike Jiang ,Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowWorkspace
Branch: RELEASE_3_12
Last Commit: 6af477a
Last Changed Date: 2020-10-27 10:41:36 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowWorkspace
Version: 4.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowWorkspace
StartedAt: 2021-05-05 16:20:04 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:23:31 -0400 (Wed, 05 May 2021)
EllapsedTime: 206.9 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL flowWorkspace
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘flowWorkspace’ ...
** using staged installation
** libs
make: R: Command not found
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_API.cpp -o R_API.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_API.cpp:9:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from R_GatingHierarchy.cpp:17:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_GatingSet.cpp -o R_GatingSet.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from R_GatingSet.cpp:10:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace.h:5,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from ../inst/include/flowWorkspace.h:6,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
RcppExports.cpp:607:45:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytoframeAPI.cpp -o cytoframeAPI.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytoframeAPI.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytoframeAPI.cpp:3:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytoframeAPI.cpp:9:45:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cytosetAPI.cpp -o cytosetAPI.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/H5CytoFrame.hpp:12,
                 from cytosetAPI.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp.h:46:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:34,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:15,
                 from cytosetAPI.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h: In instantiation of ‘void Rcpp::standard_delete_finalizer(T*) [with T = cytolib::CytoFrameView]’:
cytosetAPI.cpp:38:81:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include/Rcpp/XPtr.h:30:5: warning: deleting object of polymorphic class type ‘cytolib::CytoFrameView’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
     delete obj;
     ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getDescendants.cpp -o getDescendants.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getDescendants.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getPopStats.cpp -o getPopStats.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getPopStats.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from getSingleCellExpression.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c h5_error_r_handler.cpp -o h5_error_r_handler.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from ../inst/include/flowWorkspace/pairVectorRcppWrap.h:12,
                 from h5_error_r_handler.cpp:8:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c setCounts.cpp -o setCounts.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:16:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:255,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
                 from setCounts.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/home/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
mkdir -p "/home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib"
ar rs "/home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a" R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o
ar: creating /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/lib/libflowWorkspace.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowWorkspace.so; fi
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-flowWorkspace/00new/flowWorkspace/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowWorkspace)