##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/flowWorkspace_3.19.24.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=flowWorkspace.buildbin-libdir --merge-multiarch flowWorkspace_3.19.24.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL flowWorkspace_3.19.24.zip && rm flowWorkspace_3.19.24.tar.gz flowWorkspace_3.19.24.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
28 3635k 28 1026k 0 0 4026k 0 --:--:-- --:--:-- --:--:-- 4088k
100 3635k 100 3635k 0 0 12.7M 0 --:--:-- --:--:-- --:--:-- 12.9M
install for i386
* installing *source* package 'flowWorkspace' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.cpp -o GatingSet.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
C:/protobuf-2.6.1-newtoolchain//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
In file included from include/POPINDICES.hpp:15:0,
from POPINDICES.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_API.cpp -o R_API.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from R_API.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from R_GatingHierarchy.cpp:17:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from R_GatingSet.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/../../src/include/POPINDICES.hpp:15:0,
from ../inst/include/../../src/include/nodeProperties.hpp:11,
from ../inst/include/../../src/include/populationTree.hpp:11,
from ../inst/include/../../src/include/GatingHierarchy.hpp:13,
from ../inst/include/../../src/include/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
../inst/include/../../src/include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
../inst/include/../../src/include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
../inst/include/../../src/include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
../inst/include/../../src/include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c compensation.cpp -o compensation.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowData.cpp -o flowData.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:0:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
gate.cpp: In member function 'void CurlyGuadGate::interpolate(trans_local&)':
gate.cpp:1160:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
gate.cpp:1167:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c global.cpp -o global.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c spline.cpp -o spline.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c transformation.cpp -o transformation.o
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'logTrans::logTrans()':
include/transformation.hpp:229:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
include/transformation.hpp:228:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:273:1: warning: when initialized here [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'logTrans::logTrans(double, double, unsigned int, unsigned int)':
include/transformation.hpp:229:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
include/transformation.hpp:228:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:278:1: warning: when initialized here [-Wreorder]
logTrans::logTrans(double _offset,double _decade, unsigned _T, unsigned _scale):transformation(false,LOG),offset(_offset),decade(_decade),T(_T), scale(_scale){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans()':
include/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length,T, A, M;
^
include/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;//unused at this moment
^
transformation.cpp:281:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans(double, double, double, double, double)':
include/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length,T, A, M;
^
include/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;//unused at this moment
^
transformation.cpp:285:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans(double _length, double _maxRange, double _T, double _A, double _M):transformation(false, FASINH),length(_length),maxRange(_maxRange), T(_T),A(_A),M(_M){
^
transformation.cpp: In member function 'virtual void logInverseTrans::transforming(std::valarray<double>&)':
transformation.cpp:431:10: warning: unused variable 'thisMin' [-Wunused-variable]
double thisMin=0;//input.min();
^
transformation.cpp: In member function 'virtual void biexpTrans::computCalTbl()':
transformation.cpp:590:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < nPoints; j++)
^
transformation.cpp:603:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(zeroChan<0||zeroChan>=nPoints)
^
transformation.cpp:607:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = zeroChan; j < nPoints; j++)
^
transformation.cpp:611:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(m<0||m>=nPoints)
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:561:27: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
include/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
include/gate.hpp:414:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
winFlowJoWorkspace.cpp:538:7: note: 'quad' was declared here
QUAD quad;
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c workspace.cpp -o workspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//i386/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c wsNode.cpp -o wsNode.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o compensation.o delimitedMessage.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o c:/libxml2//i386/lib/libxml2.a C:/protobuf-2.6.1-newtoolchain//i386/lib/libprotobuf.a D:/biocbld/bbs-3.4-bioc/R/library/flowCore/lib/i386/libboost_regex.a -lws2_32 -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** 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 'flowWorkspace' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.cpp -o GatingSet.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
C:/protobuf-2.6.1-newtoolchain//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c POPINDICES.cpp -o POPINDICES.o
In file included from include/POPINDICES.hpp:15:0,
from POPINDICES.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_API.cpp -o R_API.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from R_API.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from R_GatingHierarchy.cpp:17:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from R_GatingSet.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/../../src/include/POPINDICES.hpp:15:0,
from ../inst/include/../../src/include/nodeProperties.hpp:11,
from ../inst/include/../../src/include/populationTree.hpp:11,
from ../inst/include/../../src/include/GatingHierarchy.hpp:13,
from ../inst/include/../../src/include/GatingSet.hpp:12,
from ../inst/include/flowWorkspace.h:5,
from RcppExports.cpp:4:
../inst/include/../../src/include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
../inst/include/../../src/include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
../inst/include/../../src/include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
../inst/include/../../src/include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c compensation.cpp -o compensation.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowData.cpp -o flowData.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:0:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
gate.cpp: In member function 'void CurlyGuadGate::interpolate(trans_local&)':
gate.cpp:1160:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
gate.cpp:1167:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c global.cpp -o global.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c nodeProperties.cpp -o nodeProperties.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c spline.cpp -o spline.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c transformation.cpp -o transformation.o
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'logTrans::logTrans()':
include/transformation.hpp:229:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
include/transformation.hpp:228:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:273:1: warning: when initialized here [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'logTrans::logTrans(double, double, unsigned int, unsigned int)':
include/transformation.hpp:229:12: warning: 'logTrans::T' will be initialized after [-Wreorder]
unsigned T; //top value; derived from keyword $PnR for each channel
^
include/transformation.hpp:228:12: warning: 'unsigned int logTrans::scale' [-Wreorder]
unsigned scale;
^
transformation.cpp:278:1: warning: when initialized here [-Wreorder]
logTrans::logTrans(double _offset,double _decade, unsigned _T, unsigned _scale):transformation(false,LOG),offset(_offset),decade(_decade),T(_T), scale(_scale){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans()':
include/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length,T, A, M;
^
include/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;//unused at this moment
^
transformation.cpp:281:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
^
In file included from transformation.cpp:8:0:
include/transformation.hpp: In constructor 'fasinhTrans::fasinhTrans(double, double, double, double, double)':
include/transformation.hpp:190:9: warning: 'fasinhTrans::length' will be initialized after [-Wreorder]
double length,T, A, M;
^
include/transformation.hpp:189:9: warning: 'double fasinhTrans::maxRange' [-Wreorder]
double maxRange;//unused at this moment
^
transformation.cpp:285:1: warning: when initialized here [-Wreorder]
fasinhTrans::fasinhTrans(double _length, double _maxRange, double _T, double _A, double _M):transformation(false, FASINH),length(_length),maxRange(_maxRange), T(_T),A(_A),M(_M){
^
transformation.cpp: In member function 'virtual void logInverseTrans::transforming(std::valarray<double>&)':
transformation.cpp:431:10: warning: unused variable 'thisMin' [-Wunused-variable]
double thisMin=0;//input.min();
^
transformation.cpp: In member function 'virtual void biexpTrans::computCalTbl()':
transformation.cpp:590:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = 0; j < nPoints; j++)
^
transformation.cpp:603:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(zeroChan<0||zeroChan>=nPoints)
^
transformation.cpp:607:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int j = zeroChan; j < nPoints; j++)
^
transformation.cpp:611:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(m<0||m>=nPoints)
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:561:27: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
^
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
include/gate.hpp: In member function 'CurlyGuadGate* winFlowJoWorkspace::getGate(wsCurlyQuadGateNode&)':
include/gate.hpp:414:94: warning: 'quad' may be used uninitialized in this function [-Wmaybe-uninitialized]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
winFlowJoWorkspace.cpp:538:7: note: 'quad' was declared here
QUAD quad;
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c workspace.cpp -o workspace.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -IC:/protobuf-2.6.1-newtoolchain//x64/include -DLIBXML_STATIC -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/BH/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c wsNode.cpp -o wsNode.o
In file included from include/POPINDICES.hpp:15:0,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:412:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:411:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:414:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o flowWorkspace.dll tmp.def GatingHierarchy.o GatingSet.o GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o compensation.o delimitedMessage.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o c:/libxml2//x64/lib/libxml2.a C:/protobuf-2.6.1-newtoolchain//x64/lib/libprotobuf.a D:/biocbld/bbs-3.4-bioc/R/library/flowCore/lib/x64/libboost_regex.a -lws2_32 -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.19.24.zip
* DONE (flowWorkspace)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'flowWorkspace' successfully unpacked and MD5 sums checked
