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CHECK report for cytolib on malbec1

This page was generated on 2021-05-06 12:27:17 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the cytolib package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 416/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cytolib 2.2.1  (landing page)
Mike Jiang , Jake Wagner
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/cytolib
Branch: RELEASE_3_12
Last Commit: fb08852
Last Changed Date: 2021-01-16 23:24:00 -0400 (Sat, 16 Jan 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: cytolib
Version: 2.2.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cytolib_2.2.1.tar.gz
StartedAt: 2021-05-06 00:37:29 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:37:45 -0400 (Thu, 06 May 2021)
EllapsedTime: 15.7 seconds
RetCode: 0
Status:   OK  
CheckDir: cytolib.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:cytolib.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings cytolib_2.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/cytolib.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cytolib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cytolib’ version ‘2.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
  cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cytolib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/cytolib/libs/cytolib.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/cytolib.Rcheck/00check.log’
for details.

Installation output

cytolib.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config knows TileDB... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.2.1
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
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/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 CytoFrame.cpp -o CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 CytoFrameView.cpp -o CytoFrameView.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/CytoFrameView.hpp:12,
                 from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 CytoVFS.cpp -o CytoVFS.o
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/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 GatingHierarchy.cpp -o GatingHierarchy.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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 ../inst/include/cytolib/populationTree.hpp:14,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from GatingHierarchy.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>")
                                     ^
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/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 GatingSet.cpp -o GatingSet.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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 ../inst/include/cytolib/populationTree.hpp:14,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.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 ../inst/include/cytolib/compensation.hpp:19:0,
                 from ../inst/include/cytolib/CytoFrame.hpp:16,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from ../inst/include/cytolib/populationTree.hpp:13,
                 from ../inst/include/cytolib/GatingHierarchy.hpp:17,
                 from ../inst/include/cytolib/GatingSet.hpp:14,
                 from GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor ‘cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, cytolib::CytoCtx)’:
../inst/include/cytolib/global.hpp:29:3: warning: ‘fmt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   switch(fmt)
   ^~~~~~
GatingSet.cpp:30:14: note: ‘fmt’ was declared here
   FileFormat fmt;
              ^~~
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/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 GatingSet.pb.cc -o GatingSet.pb.o
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/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 H5CytoFrame.cpp -o H5CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/H5CytoFrame.hpp:12,
                 from H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:551:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
      #pragma omp parallel for
 
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 POPINDICES.cpp -o POPINDICES.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 calibrationTable.cpp -o calibrationTable.o
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/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 compensation.cpp -o compensation.o
In file included from compensation.cpp:3:0:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 dummy.cpp -o dummy.o
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/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 ellipse2points.cpp -o ellipse2points.o
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/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 gate.cpp -o gate.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 global.cpp -o global.o
global.cpp: In function ‘std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)’:
global.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 1; i < tokens.size(); i++)
                  ~~^~~~~~~~~~~~~~~
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/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 in_polygon.cpp -o in_polygon.o
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/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 nodeProperties.cpp -o nodeProperties.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 from ../inst/include/cytolib/MemCytoFrame.hpp:12,
                 from ../inst/include/cytolib/gate.hpp:12,
                 from ../inst/include/cytolib/POPINDICES.hpp:14,
                 from ../inst/include/cytolib/nodeProperties.hpp:13,
                 from nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/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)
                               ~~^~~~~~~~~~~~~~~~~~~~~
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/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 spline.cpp -o spline.o
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/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 trans_group.cpp -o trans_group.o
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/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 transformation.cpp -o transformation.o
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/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 boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
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/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 boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
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/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 boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
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/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 boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
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/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 boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
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/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 boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
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/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 boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
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/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 boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
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/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 boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
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/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 boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
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/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 boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o cytolib.so CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.o ellipse2points.o gate.o global.o in_polygon.o nodeProperties.o spline.o trans_group.o transformation.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/portability.o boost/libs/system/src/error_code.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_cpp.a /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
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-cytolib/00new/cytolib/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 (cytolib)

Tests output

Example timings