##############################################################################
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###
### Running command:
###
### rm -rf flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && mkdir flowWorkspace.buildbin-libdir flowWorkspace.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.24.4.tar.gz >flowWorkspace.Rcheck\00install.out 2>&1 && cp flowWorkspace.Rcheck\00install.out flowWorkspace-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=flowWorkspace.buildbin-libdir --install="check:flowWorkspace-install.out" --force-multiarch --no-vignettes --timings flowWorkspace_3.24.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '3.24.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'flowWorkspace' can be installed ... OK
* checking installed package size ... NOTE
installed size is 16.7Mb
sub-directories of 1Mb or more:
lib 8.0Mb
libs 7.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'BH' is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'RSVGTipsDevice' 'parallel'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
'RBGL' 'graphics'
All declared Imports should be used.
Unexported objects imported by ':::' calls:
'Rgraphviz:::getRenderPar' 'flowCore:::.estimateLogicle'
'flowCore:::checkClass' 'flowCore:::copyFlowSet' 'flowCore:::guid'
'flowCore:::logicle_transform' 'graph:::.makeEdgeKeys'
'lattice:::updateList' 'ncdfFlow:::.isValidSamples'
'stats:::.splinefun'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.load_gs' '.preprocessMap' '.uuid_gen' 'isNegated'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GatingSet,GatingHierarchy-character: warning in list.files(pattern =
paste("^", file, "$", sep = ""), path = path, recursive = TRUE, full
= TRUE): partial argument match of 'full' to 'full.names'
getGate,GatingSetList-character: warning in unlist(res, recur = FALSE):
partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for 'is'
.computeCV : <anonymous>: no visible binding for global variable
'xml.count'
.computeCV : <anonymous>: no visible binding for global variable
'openCyto.count'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'IQR'
.computeCV : <anonymous> : <anonymous>: no visible global function
definition for 'median'
.computeCV_gh : <anonymous>: no visible global function definition for
'IQR'
.computeCV_gh : <anonymous>: no visible global function definition for
'median'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable 'max_val'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable 'decade'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable 'offset'
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
global variable 'min_val'
.convertTrans : <anonymous>: multiple local function definitions for
'f' with different formal arguments
.dropRedundantNodes : <anonymous>: no visible global function
definition for 'is'
.graph_handler : asGraphNEL: no visible global function definition for
'new'
.graph_handler : asGraphNEL: no visible global function definition for
'validObject'
.load_gs: no visible global function definition for 'new'
.load_gs: no visible global function definition for '.hasSlot'
.load_gs: no visible global function definition for 'slot'
.mergeGates : <anonymous>: no visible global function definition for
'extends'
.parse.pData: no visible binding for global variable '.'
.plotGate: no visible global function definition for 'new'
.plotGate: no visible global function definition for 'as.formula'
.plotGatingTree: no visible global function definition for 'dev.prev'
.plotGatingTree: no visible global function definition for 'dev.off'
.plotGatingTree: no visible global function definition for 'dev.set'
.preplot: no visible global function definition for 'as'
.preprocessMap: no visible binding for global variable 'old'
.preprocessMap: no visible binding for global variable '.'
.preprocessor: no visible binding for global variable 'groupName'
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for 'symbols'
.renderNodes.svgAnno: no visible global function definition for 'rect'
.renderNodes.svgAnno : <anonymous>: no visible global function
definition for 'polygon'
.renderNodes.svgAnno: no visible global function definition for
'polygon'
.renderNodes.svgAnno: no visible global function definition for
'strwidth'
.renderNodes.svgAnno: no visible global function definition for
'strheight'
.renderNodes.svgAnno: no visible global function definition for
'dev.prev'
.renderNodes.svgAnno: no visible global function definition for
'dev.off'
.renderNodes.svgAnno: no visible global function definition for
'dev.set'
.renderNodes.svgAnno: no visible global function definition for 'text'
GatingSetList: no visible global function definition for 'as'
GatingSetList: no visible global function definition for 'validObject'
booleanFilter: no visible global function definition for 'new'
char2booleanFilter: no visible global function definition for 'new'
dropRedundantNodes : <anonymous>: no visible global function definition
for 'is'
flowWorkspace.par.init: no visible global function definition for
'gray'
getMergedStats: no visible binding for global variable 'sampleName'
mkformula: no visible global function definition for 'as.formula'
save_gslist: no visible binding for global variable 'slot'
transformerList: no visible global function definition for 'is'
transformerList: no visible binding for global variable 'is'
GatingSet,GatingHierarchy-character: no visible global function
definition for 'new'
GatingSet,character-character: no visible global function definition
for 'new'
GatingSet,flowSet-ANY: no visible global function definition for 'new'
Rm,character-GatingSetList-character: no visible global function
definition for 'selectMethod'
[,GatingSet-ANY: no visible global function definition for 'extends'
[,GatingSetList-ANY: no visible global function definition for
'callNextMethod'
[,GatingSetList-ANY: no visible global function definition for 'as'
[[,GatingSet-character: no visible global function definition for 'new'
add,GatingSet-filtersList: no visible global function definition for
'selectMethod'
add,GatingSet-list : <anonymous>: no visible global function definition
for 'extends'
add,GatingSet-list: no visible global function definition for
'selectMethod'
add,GatingSetList-filter: no visible global function definition for
'selectMethod'
add,GatingSetList-filterList: no visible global function definition for
'selectMethod'
add,GatingSetList-filters: no visible global function definition for
'selectMethod'
add,GatingSetList-filtersList: no visible global function definition
for 'selectMethod'
add,GatingSetList-list: no visible global function definition for
'selectMethod'
getPopStats,GatingHierarchy: no visible binding for global variable
'node'
keyword,GatingSetList-character: no visible global function definition
for 'selectMethod'
keyword,GatingSetList-missing: no visible global function definition
for 'selectMethod'
openWorkspace,character: no visible global function definition for
'new'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'callNextMethod'
pData<-,GatingSetList-data.frame: no visible global function definition
for 'as'
plotGate,GatingSetList-character: no visible global function definition
for 'selectMethod'
rbind2,GatingSetList-missing: no visible global function definition for
'new'
rbind2,GatingSetList-missing: no visible binding for global variable
'slot'
recompute,GatingSetList: no visible global function definition for
'selectMethod'
transform,GatingSet: no visible global function definition for 'is'
Undefined global functions or variables:
. .hasSlot IQR as as.formula callNextMethod decade dev.off dev.prev
dev.set extends gray groupName is max_val median min_val new node
offset old openCyto.count polygon rect sampleName selectMethod slot
strheight strwidth symbols text validObject xml.count
Consider adding
importFrom("grDevices", "dev.off", "dev.prev", "dev.set", "gray")
importFrom("graphics", "polygon", "rect", "strheight", "strwidth",
"symbols", "text")
importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
"is", "new", "selectMethod", "slot", "validObject")
importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/flowWorkspace.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GatingHierarchy-class 5.16 0.27 6.33
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'flowWorkspace' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace"
cp include/* C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace -f
cp GatingSet.pb.h C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include -f #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
c:/protobuf//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//i386/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
c:/protobuf//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//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//i386/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
c:/protobuf//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//i386/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
c:/protobuf//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//i386/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
c:/protobuf//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//i386/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
c:/protobuf//i386/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//i386/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
c:/protobuf//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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
../inst/include/../../src/include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
../inst/include/../../src/include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c compensation.cpp -o compensation.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ellipse2points.cpp -o ellipse2points.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c flowData.cpp -o flowData.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: 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:1103:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
gate.cpp:1110:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getSingleCellExpression.cpp -o getSingleCellExpression.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 getSingleCellExpression.cpp:2:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
getSingleCellExpression.cpp: In function 'Rcpp::NumericMatrix getSingleCellExpressionByGate(Rcpp::XPtr<GatingSet>, std::string, Rcpp::List, Rcpp::NumericMatrix, Rcpp::CharacterVector, bool)':
getSingleCellExpression.cpp:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned j = 0; j < pops.size(); ++j){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c global.cpp -o global.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c spline.cpp -o spline.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: 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:440:94: 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//i386/include/libxml2 -Ic:/protobuf//i386/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a" 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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/i386/libflowWorkspace.a
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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.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//i386/lib/libprotobuf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/flowCore/lib/i386/libboost_regex.a -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/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
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace"
cp include/* C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace -f
cp GatingSet.pb.h C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include -f #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GatingSet.pb.cc -o GatingSet.pb.o
In file included from GatingSet.pb.cc:12:0:
c:/protobuf//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//x64/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
c:/protobuf//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//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//x64/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
c:/protobuf//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//x64/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
c:/protobuf//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//x64/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
c:/protobuf//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//x64/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
c:/protobuf//x64/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
c:/protobuf//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//x64/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
c:/protobuf//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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
../inst/include/../../src/include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
../inst/include/../../src/include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c calibrationTable.cpp -o calibrationTable.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c compensation.cpp -o compensation.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c delimitedMessage.cpp -o delimitedMessage.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ellipse2points.cpp -o ellipse2points.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c flowData.cpp -o flowData.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: 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:1103:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
gate.cpp:1110:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nLen; i++){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getSingleCellExpression.cpp -o getSingleCellExpression.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 getSingleCellExpression.cpp:2:
include/gate.hpp: In constructor 'CurlyGuadGate::CurlyGuadGate(paramPoly, QUAD)':
include/gate.hpp:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c global.cpp -o global.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c spline.cpp -o spline.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: 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:440:94: 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -DROUT -Ic:/libxml2//x64/include/libxml2 -Ic:/protobuf//x64/include -DLIBXML_STATIC -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c 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:438:7: warning: 'CurlyGuadGate::quadrant' will be initialized after [-Wreorder]
QUAD quadrant;
^
include/gate.hpp:437:7: warning: 'bool CurlyGuadGate::interpolated' [-Wreorder]
bool interpolated;
^
include/gate.hpp:440:2: warning: when initialized here [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a" 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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/x64/libflowWorkspace.a
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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.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//x64/lib/libprotobuf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/flowCore/lib/x64/libboost_regex.a -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowWorkspace' as flowWorkspace_3.24.4.zip
* DONE (flowWorkspace)
