BioC 3.6: BUILD BIN report for flowWorkspace on veracruz1

Package: flowWorkspace

Version: 3.25.7

Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.25.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir

StartedAt: 2017-08-16 10:23:59 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 10:27:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 213.9 seconds

RetCode: 0

Status:  OK

PackageFile: flowWorkspace_3.25.7.tgz

PackageFileSize: 10.34 MiB

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###
### Running command:
###
###   rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.25.7.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.25.7.tar.gz'
>>>>>>> 

* installing *source* package ‘flowWorkspace’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace"
cp include/* /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include/flowWorkspace
cp GatingSet.pb.h /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/include #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from GatingHierarchy.cpp:8:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
R_GatingHierarchy.cpp:326:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)
           ˜^˜
R_GatingHierarchy.cpp:445:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:475:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:486:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:495:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
6 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from ./../inst/include/../../src/include/GatingSet.hpp:12:
In file included from ./../inst/include/../../src/include/GatingHierarchy.hpp:13:
In file included from ./../inst/include/../../src/include/populationTree.hpp:11:
In file included from ./../inst/include/../../src/include/nodeProperties.hpp:11:
In file included from ./../inst/include/../../src/include/POPINDICES.hpp:15:
./../inst/include/../../src/include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c compensation.cpp -o compensation.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c flowData.cpp -o flowData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from flowJoWorkspace.cpp:7:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:2:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c global.cpp -o global.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from macFlowJoWorkspace.cpp:9:
In file included from ./include/macFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from nodeProperties.cpp:7:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c transformation.cpp -o transformation.o
transformation.cpp:273:68: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
                                                                   ^
transformation.cpp:278:139: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans(double _offset,double _decade, unsigned _T, unsigned _scale):transformation(false,LOG),offset(_offset),decade(_decade),T(_T), scale(_scale){
                                                                                                                                          ^
transformation.cpp:281:57: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
                                                        ^
transformation.cpp:285:123: warning: field 'length' will be initialized after field 'maxRange' [-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:431:10: warning: unused variable 'thisMin' [-Wunused-variable]
                double thisMin=0;//input.min();
                       ^
5 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
In file included from winFlowJoWorkspace.cpp:8:
In file included from ./include/winFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
winFlowJoWorkspace.cpp:561:27: warning: '/*' within block comment [-Wcomment]
 * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                          ^
winFlowJoWorkspace.cpp:545:10: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(quadPattern == "--")
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:553:42: note: uninitialized use occurs here
        CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                ^˜˜˜
winFlowJoWorkspace.cpp:545:7: note: remove the 'if' if its condition is always true
        else if(quadPattern == "--")
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:538:2: note: variable 'quad' is declared here
        QUAD quad;
        ^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c workspace.cpp -o workspace.o
In file included from workspace.cpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c wsNode.cpp -o wsNode.o
In file included from wsNode.cpp:10:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
1 warning generated.
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib"
ar rs "/Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/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
ar: creating archive /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/lib/libflowWorkspace.a
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowWorkspace.so 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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowCore/lib/libboost_regex.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowWorkspace)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"