Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-13 15:05:23 -0400 (Wed, 13 Oct 2021).

CHECK results for flowCore on tokay2

To the developers/maintainers of the flowCore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCore.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 647/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 2.4.0  (landing page)
Mike Jiang
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/flowCore
git_branch: RELEASE_3_13
git_last_commit: 1f5f4b6
git_last_commit_date: 2021-05-19 11:38:20 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowCore
Version: 2.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowCore_2.4.0.tar.gz
StartedAt: 2021-10-12 22:49:06 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 22:53:30 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 263.5 seconds
RetCode: 0
Status:   OK  
CheckDir: flowCore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowCore_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCore/DESCRIPTION' ... OK
* this is package 'flowCore' version '2.4.0'
* package encoding: UTF-8
* 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 ... OK
* checking whether package 'flowCore' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.3Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    data      5.0Mb
    extdata   1.1Mb
    help      1.4Mb
    libs      5.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable 'mat'
eval,compensatedParameter-missing : <anonymous>: no visible binding for
  global variable 'msv'
show,flowFrame: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output mat msv
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 contents of 'data' directory ... NOTE
Output for data("GvHD", package = "flowCore"):
  There were 36 warnings (use warnings() to see them)
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowCore/libs/i386/flowCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/flowCore/libs/x64/flowCore.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
biexponentialTransform 5.64   0.07     5.7
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
biexponentialTransform 5.47   0.05    5.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.Rcheck/00check.log'
for details.



Installation output

flowCore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowCore_2.4.0.tar.gz && rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCore.buildbin-libdir flowCore_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowCore_2.4.0.zip && rm flowCore_2.4.0.tar.gz flowCore_2.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  8 8843k    8  726k    0     0  1480k      0  0:00:05 --:--:--  0:00:05 1479k
 32 8843k   32 2842k    0     0  1879k      0  0:00:04  0:00:01  0:00:03 1879k
 68 8843k   68 6022k    0     0  2404k      0  0:00:03  0:00:02  0:00:01 2405k
100 8843k  100 8843k    0     0  2756k      0  0:00:03  0:00:03 --:--:-- 2756k

install for i386

* installing *source* package 'flowCore' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FastLogicle.cpp -o FastLogicle.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Hyperlog.cpp -o Hyperlog.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Logicle.cpp -o Logicle.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c biexponential.cpp -o biexponential.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convertRawBytes.cpp -o convertRawBytes.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fcsTextParse.cpp -o fcsTextParse.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw32/include/c++/8.3.0/locale:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:8:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from fcsTextParse.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hyperlogTransform.cpp -o hyperlogTransform.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inPolygon.cpp -o inPolygon.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inPolytope.cpp -o inPolytope.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c logicleTransform.cpp -o logicleTransform.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw32/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/rtools40/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c poly_centroid.cpp -o poly_centroid.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sortBytes.cpp -o sortBytes.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c uint2double.cpp -o uint2double.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c zeroin.cpp -o zeroin.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/i386/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/i386 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lstdc++fs -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/00LOCK-flowCore/00new/flowCore/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCore'
    finding HTML links ... done
    CytoExploreR_exports                    html  
    EHtrans-class                           html  
    FCSTransTransform                       html  
    GvHD                                    html  
    Subset-methods                          html  
    arcsinhTransform                        html  
    asinht-class                            html  
    asinhtGml2-class                        html  
    biexponentialTransform                  html  
    boundaryFilter-class                    html  
    characterOrNumeric-class                html  
    characterOrParameters-class             html  
    characterOrTransformation-class         html  
    checkOffset                             html  
    coerce                                  html  
    collapse_desc                           html  
    compensatedParameter-class              html  
    compensation-class                      html  
    complementFilter-class                  html  
    concreteFilter-class                    html  
    decompensate                            html  
    dg1polynomial-class                     html  
    each_col                                html  
    ellipsoidGate-class                     html  
    estimateMedianLogicle                   html  
    exponential-class                       html  
    expressionFilter-class                  html  
    filter-and-methods                      html  
    filter-class                            html  
    filter-in-methods                       html  
    filter-methods                          html  
    filter-on-methods                       html  
    filterDetails-methods                   html  
    filterList-class                        html  
    filterReference-class                   html  
    filterResult-class                      html  
    filterResultList-class                  html  
    filterSummary-class                     html  
    filterSummaryList-class                 html  
    filters-class                           html  
    flowCore-package                        html  
    flowFrame-class                         html  
    flowSet-class                           html  
    flowSet_to_list                         html  
    fr_append_cols                          html  
    fsApply                                 html  
    getChannelMarker                        html  
    getIndexSort                            html  
    hyperlog-class                          html  
    hyperlogtGml2-class                     html  
    identifier-methods                      html  
    intersectFilter-class                   html  
    inverseLogicleTransform                 html  
    invsplitscale-class                     html  
    keyword-methods                         html  
    kmeansFilter-class                      html  
    linearTransform                         html  
    lintGml2-class                          html  
    lnTransform                             html  
    logTransform                            html  
    logarithm-class                         html  
    logicalFilterResult-class               html  
    logicleTransform                        html  
    logicletGml2-class                      html  
    logtGml2-class                          html  
    manyFilterResult-class                  html  
    markernames                             html  
    multipleFilterResult-class              html  
    normalization-class                     html  
    nullParameter-class                     html  
    parameterFilter-class                   html  
    parameterTransform-class                html  
    parameters-class                        html  
    parameters-methods                      html  
    polygonGate-class                       html  
    polytopeGate-class                      html  
    quadGate-class                          html  
    quadratic-class                         html  
    quadraticTransform                      html  
    randomFilterResult-class                html  
    ratio-class                             html  
    ratiotGml2-class                        html  
    read.FCS                                html  
    read.FCSheader                          html  
    read.flowSet                            html  
    rectangleGate-class                     html  
    rotate_gate                             html  
    sampleFilter-class                      html  
    scaleTransform                          html  
    scale_gate                              html  
    setOperationFilter-class                html  
    shift_gate                              html  
    singleParameterTransform-class          html  
    sinht-class                             html  
    split-methods                           html  
    splitScaleTransform                     html  
    splitscale-class                        html  
    squareroot-class                        html  
    subsetFilter-class                      html  
    summarizeFilter-methods                 html  
    timeFilter-class                        html  
    transform-class                         html  
    transform                               html  
    transformFilter-class                   html  
    transformList-class                     html  
    transformMap-class                      html  
    transformReference-class                html  
    transform_gate                          html  
    transformation-class                    html  
    truncateTransform                       html  
    unionFilter-class                       html  
    unitytransform-class                    html  
    updateTransformKeywords                 html  
    validFilters                            html  
    write.FCS                               html  
    write.flowSet                           html  
** building package indices
** installing vignettes
   'HowTo-flowCore.Rnw' using 'UTF-8' 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'flowCore' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FastLogicle.cpp -o FastLogicle.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Hyperlog.cpp -o Hyperlog.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Logicle.cpp -o Logicle.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from flowCore_types.h:12,
                 from RcppExports.cpp:4:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c biexponential.cpp -o biexponential.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convertRawBytes.cpp -o convertRawBytes.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fcsTextParse.cpp -o fcsTextParse.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from fcsTextParse.cpp:8:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/bits/locale_conv.h:41,
                 from C:/rtools40/mingw64/include/c++/8.3.0/locale:43,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/classification.hpp:15,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from fcsTextParse.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from fcsTextParse.cpp:10:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hyperlogTransform.cpp -o hyperlogTransform.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inPolygon.cpp -o inPolygon.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inPolytope.cpp -o inPolytope.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c logicleTransform.cpp -o logicleTransform.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/function.hpp:30,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:141,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
                 from C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
                 from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from pairVectorRcppWrap.h:10,
                 from pairVectorRcppWrap.cpp:7:
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c poly_centroid.cpp -o poly_centroid.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sortBytes.cpp -o sortBytes.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c uint2double.cpp -o uint2double.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c zeroin.cpp -o zeroin.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o flowCore.dll tmp.def FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o poly_centroid.o sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/cytolib/lib/x64/libcytolib.a C:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lstdc++fs -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.dll; fi
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_2.4.0.zip
* DONE (flowCore)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked

Tests output

flowCore.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowCore)
> library(flowStats)
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:flowStats':

    normalize

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

== Skipped tests ===============================================================
* dir.exists(dataPath) is not TRUE (1)
* file.exists(filename) is not TRUE (2)

[ FAIL 0 | WARN 190 | SKIP 3 | PASS 334 ]
There were 36 warnings (use warnings() to see them)
> 
> #devtools::test("~/rglab/workspace/flowCore")
> 
> proc.time()
   user  system elapsed 
  22.71    2.03   25.82 

flowCore.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowCore)
> library(flowStats)
> 
> 
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:flowStats':

    normalize

The following object is masked from 'package:flowCore':

    normalize

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

== Skipped tests ===============================================================
* dir.exists(dataPath) is not TRUE (1)
* file.exists(filename) is not TRUE (2)

[ FAIL 0 | WARN 190 | SKIP 3 | PASS 334 ]
There were 36 warnings (use warnings() to see them)
> 
> #devtools::test("~/rglab/workspace/flowCore")
> 
> proc.time()
   user  system elapsed 
  19.25    1.43   21.00 

Example timings

flowCore.Rcheck/examples_i386/flowCore-Ex.timings

nameusersystemelapsed
EHtrans-class0.030.020.05
FCSTransTransform0.780.010.79
Subset-methods0.190.000.19
arcsinhTransform0.040.000.05
asinht-class0.000.020.01
asinhtGml2-class0.030.010.05
biexponentialTransform5.640.075.70
boundaryFilter-class0.180.020.19
characterOrNumeric-class000
characterOrParameters-class000
characterOrTransformation-class000
coerce0.030.010.04
collapse_desc0.680.020.71
compensatedParameter-class0.190.000.31
compensation-class0.440.040.48
decompensate0.050.020.07
dg1polynomial-class0.040.000.04
each_col0.030.000.03
ellipsoidGate-class0.060.020.08
exponential-class0.030.000.03
expressionFilter-class0.080.000.08
filter-methods1.140.011.15
filter-on-methods0.080.000.08
filterList-class000
filterResult-class000
filterResultList-class4.050.164.21
filterSummary-class0.080.010.09
filterSummaryList-class1.020.131.15
flowFrame-class4.450.094.54
flowSet-class2.420.222.64
fr_append_cols0.720.050.77
fsApply0.130.000.12
getIndexSort0.010.000.02
hyperlog-class0.910.000.91
hyperlogtGml2-class0.010.000.01
identifier-methods0.030.000.03
inverseLogicleTransform0.750.030.78
invsplitscale-class0.040.000.03
keyword-methods0.900.060.97
kmeansFilter-class0.130.000.13
linearTransform0.030.000.03
lintGml2-class0.030.000.03
lnTransform1.640.061.70
logTransform0.030.000.04
logarithm-class0.030.000.03
logicalFilterResult-class000
logicleTransform0.800.040.82
logicletGml2-class0.060.000.07
logtGml2-class0.030.000.03
manyFilterResult-class000
markernames0.690.090.78
multipleFilterResult-class000
parameters-methods0.020.000.02
polygonGate-class0.060.000.06
quadGate-class0.140.000.14
quadratic-class0.020.000.01
quadraticTransform0.030.000.04
ratio-class0.010.010.03
ratiotGml2-class0.030.000.03
read.FCS0.080.000.08
read.FCSheader000
read.flowSet0.440.000.43
rectangleGate-class0.060.000.07
rotate_gate000
sampleFilter-class0.050.000.04
scaleTransform0.030.000.03
scale_gate000
shift_gate000
singleParameterTransform-class000
sinht-class0.030.000.04
split-methods0.990.021.00
splitScaleTransform1.000.051.04
splitscale-class0.010.000.02
squareroot-class0.030.000.03
timeFilter-class1.300.011.31
transform-class000
transform1.080.051.13
transformFilter-class0.110.000.11
transformList-class0.650.060.71
transformMap-class000
transform_gate000
truncateTransform0.010.000.02
unitytransform-class0.020.020.03
write.FCS0.030.000.03
write.flowSet0.820.040.88

flowCore.Rcheck/examples_x64/flowCore-Ex.timings

nameusersystemelapsed
EHtrans-class0.060.000.06
FCSTransTransform0.720.030.75
Subset-methods0.280.000.29
arcsinhTransform0.060.000.06
asinht-class0.030.000.03
asinhtGml2-class0.050.000.05
biexponentialTransform5.470.055.51
boundaryFilter-class0.080.000.08
characterOrNumeric-class000
characterOrParameters-class000
characterOrTransformation-class000
coerce0.060.000.06
collapse_desc0.860.050.91
compensatedParameter-class0.140.010.15
compensation-class0.310.030.35
decompensate0.050.000.05
dg1polynomial-class0.030.000.03
each_col0.030.000.03
ellipsoidGate-class0.060.000.06
exponential-class0.030.000.03
expressionFilter-class0.080.020.10
filter-methods0.770.030.79
filter-on-methods0.120.000.13
filterList-class000
filterResult-class000
filterResultList-class4.690.234.92
filterSummary-class0.090.000.09
filterSummaryList-class0.850.080.92
flowFrame-class4.500.084.58
flowSet-class2.300.082.38
fr_append_cols0.590.050.64
fsApply0.140.000.14
getIndexSort0.030.000.03
hyperlog-class101
hyperlogtGml2-class0.030.000.03
identifier-methods0.020.000.02
inverseLogicleTransform0.530.030.56
invsplitscale-class0.030.000.03
keyword-methods0.450.080.53
kmeansFilter-class0.110.000.11
linearTransform0.010.010.03
lintGml2-class0.040.000.03
lnTransform0.750.080.83
logTransform0.030.000.03
logarithm-class0.030.000.03
logicalFilterResult-class000
logicleTransform0.760.030.80
logicletGml2-class0.080.000.08
logtGml2-class0.030.000.03
manyFilterResult-class000
markernames0.550.050.59
multipleFilterResult-class000
parameters-methods0.030.000.03
polygonGate-class0.060.000.06
quadGate-class0.570.000.57
quadratic-class0.010.000.01
quadraticTransform0.020.000.01
ratio-class0.030.000.03
ratiotGml2-class0.030.000.04
read.FCS0.060.000.06
read.FCSheader0.020.000.01
read.flowSet0.080.000.08
rectangleGate-class0.070.000.08
rotate_gate000
sampleFilter-class0.040.000.03
scaleTransform0.030.000.03
scale_gate000
shift_gate000
singleParameterTransform-class000
sinht-class0.030.000.03
split-methods0.720.000.72
splitScaleTransform0.720.030.75
splitscale-class0.010.000.02
squareroot-class0.020.020.03
timeFilter-class1.430.051.48
transform-class000
transform0.850.040.89
transformFilter-class0.120.000.13
transformList-class0.460.050.50
transformMap-class000
transform_gate000
truncateTransform0.020.000.01
unitytransform-class0.010.000.01
write.FCS0.030.000.03
write.flowSet0.770.030.80