BioC 3.5: CHECK report for flowCore on tokay2

Package: flowCore

Version: 1.42.3

Command: rm -rf flowCore.buildbin-libdir flowCore.Rcheck && mkdir flowCore.buildbin-libdir flowCore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCore.buildbin-libdir flowCore_1.42.3.tar.gz >flowCore.Rcheck\00install.out 2>&1 && cp flowCore.Rcheck\00install.out flowCore-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=flowCore.buildbin-libdir --install="check:flowCore-install.out" --force-multiarch --no-vignettes --timings flowCore_1.42.3.tar.gz

StartedAt: 2017-10-17 23:47:17 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:54:01 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 404.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowCore.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf flowCore.buildbin-libdir flowCore.Rcheck && mkdir flowCore.buildbin-libdir flowCore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCore.buildbin-libdir flowCore_1.42.3.tar.gz >flowCore.Rcheck\00install.out 2>&1 && cp flowCore.Rcheck\00install.out flowCore-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=flowCore.buildbin-libdir --install="check:flowCore-install.out" --force-multiarch --no-vignettes --timings flowCore_1.42.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.42.3'
* 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 14.4Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    extdata   1.1Mb
    lib       3.4Mb
    libs      2.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'BH' is only usable in R >= 3.0.2
* 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 ... NOTE
'library' or 'require' call to 'Rgraphviz' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rbind2,flowSet-flowSet: warning in assign(i, x[[i]], env = env):
  partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet: warning in assign(i, y[[i]], env = env):
  partial argument match of 'env' to 'envir'
%in%,flowFrame-norm2Filter: no visible global function definition for
  'cov.rob'
spillover,flowSet: no visible global function definition for
  'devAskNewPage'
spillover,flowSet : <anonymous>: no visible global function definition
  for 'rangeGate'
spillover,flowSet : <anonymous>: no visible global function definition
  for 'density'
spillover,flowSet : <anonymous>: no visible global function definition
  for 'abline'
spillover,flowSet : <anonymous> : <anonymous>: no visible global
  function definition for 'density'
split,flowFrame-factor: no visible binding for global variable 'i'
summary,workFlow: no visible binding for global variable 'wf'
Undefined global functions or variables:
  abline cov.rob density devAskNewPage i rangeGate wf
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline")
  importFrom("stats", "density")
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 ... WARNING
Codoc mismatches from documentation object 'read.flowSet':
read.flowSet
  Code: function(files = NULL, path = ".", pattern = NULL, phenoData,
                 descriptions, name.keyword, alter.names = FALSE,
                 transformation = "linearize", which.lines = NULL,
                 column.pattern = NULL, invert.pattern = FALSE, decades
                 = 0, sep = "\t", as.is = TRUE, name, ncdf = FALSE,
                 dataset = NULL, min.limit = NULL, truncate_max_range =
                 TRUE, emptyValue = TRUE, ignore.text.offset = FALSE,
                 ...)
  Docs: function(files = NULL, path = ".", pattern = NULL, phenoData,
                 descriptions, name.keyword, alter.names = FALSE,
                 transformation = "linearize", which.lines = NULL,
                 column.pattern = NULL, invert.pattern = FALSE, decades
                 = 0, sep = "\t", as.is = TRUE, name, ncdf = FALSE,
                 dataset = NULL, min.limit = NULL, emptyValue = TRUE,
                 ignore.text.offset = FALSE, ...)
  Argument names in code not in docs:
    truncate_max_range
  Mismatches in argument names:
    Position: 19 Code: truncate_max_range Docs: emptyValue
    Position: 20 Code: emptyValue Docs: ignore.text.offset
    Position: 21 Code: ignore.text.offset Docs: ...

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'read.flowSet':
  'truncate_max_range'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.5-bioc/meat/flowCore.buildbin-libdir/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)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 or elapsed time > 5s
                       user system elapsed
biexponentialTransform 6.03   0.08    6.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
biexponentialTransform 6.94   0.06       7
* 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: 2 WARNINGs, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c biexponential.cpp -o biexponential.o
biexponential.cpp: In function 'std::vector<double> biexponential_transform(std::vector<double>, double, double, double, double, double, double, double, int)':
biexponential.cpp:52:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(i=0;i<nLen;i++) {
           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c convertRawBytes.cpp -o convertRawBytes.o
convertRawBytes.cpp: In function 'std::vector<double> convertRawBytes(BYTES, bool, std::vector<short unsigned int>, short unsigned int, bool)':
convertRawBytes.cpp:61:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nrow; i++){
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:45:80: warning: multi-line comment [-Wcomment]
    txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c hyperlogTransform.cpp -o hyperlogTransform.o
hyperlogTransform.cpp: In function 'std::vector<double> hyperlog_transform(std::vector<double>, double, double, double, double, bool)':
hyperlogTransform.cpp:26:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < nLen; i++) {
                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c logicleTransform.cpp -o logicleTransform.o
logicleTransform.cpp: In function 'std::vector<double> logicle_transform(std::vector<double>, double, double, double, double, bool)':
logicleTransform.cpp:17:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i = 0; i < nLen; i++) {
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sortBytes.cpp -o sortBytes.o
sortBytes.cpp: In function 'BYTES sortBytes(BYTES, std::vector<short unsigned int>)':
sortBytes.cpp:19:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto ind = 0; ind < nElement; ind++){
                         ^
sortBytes.cpp:20:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(auto i = 0; i < elementSize; i++){
                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/icu.cpp -o boost_regex/icu.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/instances.cpp -o boost_regex/instances.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex.cpp -o boost_regex/regex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386/libboost_regex.a
C:/Rtools/mingw_32/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 sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386/libboost_regex.a -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c FastLogicle.cpp -o FastLogicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Hyperlog.cpp -o Hyperlog.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c Logicle.cpp -o Logicle.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c biexponential.cpp -o biexponential.o
biexponential.cpp: In function 'std::vector<double> biexponential_transform(std::vector<double>, double, double, double, double, double, double, double, int)':
biexponential.cpp:52:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(i=0;i<nLen;i++) {
           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c convertRawBytes.cpp -o convertRawBytes.o
convertRawBytes.cpp: In function 'std::vector<double> convertRawBytes(BYTES, bool, std::vector<short unsigned int>, short unsigned int, bool)':
convertRawBytes.cpp:61:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto i = 0; i < nrow; i++){
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:45:80: warning: multi-line comment [-Wcomment]
    txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c hyperlogTransform.cpp -o hyperlogTransform.o
hyperlogTransform.cpp: In function 'std::vector<double> hyperlog_transform(std::vector<double>, double, double, double, double, bool)':
hyperlogTransform.cpp:26:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < nLen; i++) {
                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c inPolygon.cpp -o inPolygon.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c inPolytope.cpp -o inPolytope.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c logicleTransform.cpp -o logicleTransform.o
logicleTransform.cpp: In function 'std::vector<double> logicle_transform(std::vector<double>, double, double, double, double, bool)':
logicleTransform.cpp:17:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (int i = 0; i < nLen; i++) {
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c sortBytes.cpp -o sortBytes.o
sortBytes.cpp: In function 'BYTES sortBytes(BYTES, std::vector<short unsigned int>)':
sortBytes.cpp:19:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(auto ind = 0; ind < nElement; ind++){
                         ^
sortBytes.cpp:20:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(auto i = 0; i < elementSize; i++){
                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c uint2double.cpp -o uint2double.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c zeroin.cpp -o zeroin.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/icu.cpp -o boost_regex/icu.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/instances.cpp -o boost_regex/instances.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex.cpp -o boost_regex/regex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I../inst/include/  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64/libboost_regex.a
C:/Rtools/mingw_64/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 sortBytes.o uint2double.o zeroin.o C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64/libboost_regex.a -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.42.3.zip
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.08	0.00	0.07
FCSTransTransform	1.25	0.02	1.27
Subset-methods	0.67	0.02	0.68
actionItem-class	0	0	0
arcsinhTransform	0.1	0.0	0.1
asinht-class	0.03	0.00	0.03
asinhtGml2-class	0.03	0.01	0.04
biexponentialTransform	6.03	0.08	6.11
boundaryFilter-class	0.06	0.00	0.07
characterOrTransformation-class	0	0	0
coerce	0.07	0.00	0.06
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.32	0.00	0.33
compensation-class	0.30	0.03	0.33
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.03	0.00	0.03
ellipsoidGate	0.07	0.02	0.08
exponential-class	0.03	0.00	0.03
expressionFilter-class	0.09	0.00	0.09
fcReference-class	0	0	0
filter-methods	0.70	0.04	0.75
filter-on-methods	0.08	0.00	0.08
filterList-class	0.02	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	0	0	0
filterSummary-class	0	0	0
filterSummaryList-class	0	0	0
flowFrame-class	3.37	0.11	3.49
flowSet-class	1.94	0.05	1.99
fsApply	0.12	0.00	0.12
gateActionItem-class	0	0	0
gateView-class	0	0	0
getIndexSort-methods	0.03	0.00	0.04
hyperlog-class	1.33	0.00	1.32
hyperlogtGml2-class	0.03	0.00	0.03
identifier-methods	0.03	0.00	0.04
inverseLogicleTransform	0.63	0.05	0.67
invsplitscale-class	0.03	0.00	0.03
keyword-methods	1.06	0.03	1.09
kmeansFilter	0.25	0.00	0.25
linearTransform	0.05	0.00	0.05
lintGml2-class	0.04	0.00	0.05
lnTransform	1.46	0.03	1.48
logTransform	0.03	0.00	0.03
logarithm-class	0.03	0.00	0.03
logicalFilterResult-class	0	0	0
logicleTransform	1.13	0.05	1.18
logicletGml2-class	0.07	0.00	0.07
logtGml2-class	0.03	0.00	0.03
manyFilterResult-class	0.02	0.00	0.02
markernames	0.73	0.04	0.78
multipleFilterResult-class	0	0	0
norm2Filter-class	0.15	0.00	0.14
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.03	0.00	0.03
polygonGate	0.07	0.00	0.08
quadGate	0.16	0.00	0.15
quadratic-class	0.03	0.00	0.03
quadraticTransform	0.03	0.00	0.04
ratio-class	0.05	0.00	0.04
ratiotGml2-class	0.03	0.00	0.03
read.FCS	0.05	0.00	0.05
read.FCSheader	0.01	0.00	0.02
read.flowSet	0.10	0.00	0.09
rectangleGate	0.08	0.00	0.08
sampleFilter-class	0.04	0.00	0.05
scaleTransform	0.03	0.00	0.03
singleParameterTransform-class	0	0	0
sinht-class	0.03	0.00	0.03
split-methods	1.17	0.05	1.22
splitScaleTransform	0.99	0.06	1.05
splitscale-class	0.03	0.00	0.03
squareroot-class	0.03	0.01	0.05
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	1.44	0.05	1.48
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.14	0.00	0.14
transformList-class	0.67	0.02	0.69
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.03	0.00	0.03
unitytransform-class	0.03	0.00	0.03
view-class	0	0	0
workFlow-class	0	0	0
write.FCS	0.08	0.00	0.08
write.flowSet	1.01	0.04	1.06

name	user	system	elapsed
EHtrans-class	0.11	0.00	0.11
FCSTransTransform	1.50	0.08	1.58
Subset-methods	1.02	0.00	1.02
actionItem-class	0	0	0
arcsinhTransform	0.14	0.00	0.14
asinht-class	0.05	0.00	0.05
asinhtGml2-class	0.06	0.00	0.06
biexponentialTransform	6.94	0.06	7.00
boundaryFilter-class	0.08	0.00	0.08
characterOrTransformation-class	0	0	0
coerce	0.06	0.00	0.06
compensateActionItem-class	0	0	0
compensateView-class	0	0	0
compensatedParameter-class	0.25	0.00	0.27
compensation-class	0.45	0.02	0.47
dg1polynomial-class	0.03	0.00	0.03
each_col-methods	0.04	0.00	0.03
ellipsoidGate	0.07	0.01	0.09
exponential-class	0.04	0.00	0.03
expressionFilter-class	0.09	0.00	0.10
fcReference-class	0	0	0
filter-methods	0.76	0.00	0.76
filter-on-methods	0.1	0.0	0.1
filterList-class	0.01	0.00	0.01
filterResult-class	0	0	0
filterResultList-class	0	0	0
filterSummary-class	0	0	0
filterSummaryList-class	0	0	0
flowFrame-class	3.86	0.08	3.94
flowSet-class	2.58	0.05	2.62
fsApply	0.2	0.0	0.2
gateActionItem-class	0	0	0
gateView-class	0	0	0
getIndexSort-methods	0.05	0.00	0.05
hyperlog-class	2.84	0.01	2.86
hyperlogtGml2-class	0.05	0.00	0.05
identifier-methods	0.03	0.00	0.03
inverseLogicleTransform	0.84	0.08	0.92
invsplitscale-class	0.05	0.00	0.05
keyword-methods	0.72	0.02	0.73
kmeansFilter	0.17	0.00	0.17
linearTransform	0.03	0.00	0.03
lintGml2-class	0.03	0.00	0.04
lnTransform	1.17	0.05	1.21
logTransform	0.05	0.01	0.07
logarithm-class	0.05	0.00	0.04
logicalFilterResult-class	0	0	0
logicleTransform	1.05	0.05	1.10
logicletGml2-class	0.06	0.00	0.06
logtGml2-class	0.03	0.00	0.03
manyFilterResult-class	0	0	0
markernames	0.53	0.03	0.56
multipleFilterResult-class	0	0	0
norm2Filter-class	0.13	0.01	0.14
normalizeActionItem-class	0	0	0
normalizeView-class	0	0	0
parameters-methods	0.01	0.00	0.02
polygonGate	0.05	0.00	0.04
quadGate	0.17	0.02	0.19
quadratic-class	0.03	0.00	0.03
quadraticTransform	0.07	0.00	0.08
ratio-class	0.07	0.00	0.06
ratiotGml2-class	0.06	0.00	0.06
read.FCS	0.08	0.01	0.09
read.FCSheader	0.03	0.00	0.04
read.flowSet	0.14	0.00	0.14
rectangleGate	0.09	0.00	0.10
sampleFilter-class	0.05	0.00	0.04
scaleTransform	0.03	0.00	0.03
singleParameterTransform-class	0	0	0
sinht-class	0.03	0.00	0.03
split-methods	1.25	0.05	1.30
splitScaleTransform	1.29	0.03	1.31
splitscale-class	0.03	0.00	0.03
squareroot-class	0.04	0.00	0.05
subsettingActionItem-class	0	0	0
subsettingView-class	0	0	0
timeFilter-class	1.63	0.05	1.67
transform-class	0	0	0
transformActionItem-class	0	0	0
transformFilter-class	0.15	0.00	0.16
transformList-class	0.58	0.03	0.61
transformMap-class	0	0	0
transformView-class	0	0	0
truncateTransform	0.03	0.00	0.03
unitytransform-class	0.02	0.00	0.01
view-class	0.02	0.00	0.02
workFlow-class	0	0	0
write.FCS	0.09	0.00	0.09
write.flowSet	1.55	0.01	1.56