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BioC 3.3: INSTALL report for flowCore on moscato2

This page was generated on 2016-10-13 12:47:57 -0700 (Thu, 13 Oct 2016).

Package 395/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 1.38.2
M.Jiang
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/flowCore
Last Changed Rev: 117751 / Revision: 122332
Last Changed Date: 2016-05-20 15:21:27 -0700 (Fri, 20 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowCore
Version: 1.38.2
Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/flowCore_1.38.2.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=flowCore.buildbin-libdir --merge-multiarch flowCore_1.38.2.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL flowCore_1.38.2.zip && rm flowCore_1.38.2.tar.gz flowCore_1.38.2.zip
StartedAt: 2016-10-12 18:38:40 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 18:52:49 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 849.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/flowCore_1.38.2.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=flowCore.buildbin-libdir --merge-multiarch flowCore_1.38.2.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL flowCore_1.38.2.zip  && rm flowCore_1.38.2.tar.gz flowCore_1.38.2.zip
###
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install for i386

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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 "E:/biocbld/bbs-3.3-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "E:/biocbld/bbs-3.3-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 E:/biocbld/bbs-3.3-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 uint2double.o zeroin.o E:/biocbld/bbs-3.3-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386/libboost_regex.a -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-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
   'HowTo-flowCore.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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=c++0x -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I../inst/include/    -I"E:/biocbld/bbs-3.3-bioc/R/library/Rcpp/include" -I"E:/biocbld/bbs-3.3-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 "E:/biocbld/bbs-3.3-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "E:/biocbld/bbs-3.3-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 E:/biocbld/bbs-3.3-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 uint2double.o zeroin.o E:/biocbld/bbs-3.3-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64/libboost_regex.a -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.38.2.zip
* DONE (flowCore)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked