BioC 3.6: BUILD BIN report for CytoML on veracruz1

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### Running command:
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###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_1.3.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CytoML.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CytoML.buildbin-libdir CytoML_1.3.1.tar.gz'
>>>>>>> 

* installing *source* package ‘CytoML’ ...
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 CytoML
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
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/flowWorkspace/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 ./CytoML_types.h:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/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/flowWorkspace/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 setCounts.cpp -o setCounts.o
In file included from setCounts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingSet.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/GatingHierarchy.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/populationTree.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/POPINDICES.hpp:15:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace/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 -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 CytoML.so RcppExports.o setCounts.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RProtoBufLib/lib/libprotobuf.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowCore/lib/libboost_regex.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/CytoML.buildbin-libdir/CytoML/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (CytoML)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CytoML.buildbin-libdir/CytoML/libs//CytoML.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" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.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" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"
BioC 3.6: BUILD BIN report for CytoML on veracruz1

Summary

Command output
