flowCore 1.40.6
M.Jiang
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/flowCore | | Last Changed Rev: 127452 / Revision: 128728 | | Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/flowCore_1.40.6.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=flowCore.buildbin-libdir --merge-multiarch flowCore_1.40.6.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL flowCore_1.40.6.zip && rm flowCore_1.40.6.tar.gz flowCore_1.40.6.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 7928k 100 7928k 0 0 65.5M 0 --:--:-- --:--:-- --:--:-- 66.1M
install for i386
* installing *source* package 'flowCore' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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-3.4-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/i386/libboost_regex.a -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I../inst/include/ -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-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-3.4-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/x64/libboost_regex.a -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/flowCore.buildbin-libdir/flowCore/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCore' as flowCore_1.40.6.zip
* DONE (flowCore)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'flowCore' successfully unpacked and MD5 sums checked