Package: CytoML

Version: 1.12.1

Command: rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_1.12.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CytoML.buildbin-libdir

StartedAt: 2020-04-15 07:14:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:16:16 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 102.1 seconds

RetCode: 0

Status:  OK

PackageFile: CytoML_1.12.1.tgz

PackageFileSize: 9.593 MiB

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### Running command:
###
###   rm -rf CytoML.buildbin-libdir && mkdir CytoML.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CytoML_1.12.1.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_1.12.1.tar.gz'
>>>>>>> 

* installing *source* package ‘CytoML’ ...
** using staged installation
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
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../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:14:
In file included from ../inst/include/flowWorkspace/wsNode.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^~~~~~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:808:12: warning: unused variable 'minRange' [-Wunused-variable]
                                double minRange=atof(transNode.getProperty("minRange").c_str());
                                       ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/CytoML.h:5:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/vector:270:
In file included from /usr/local/clang7/include/c++/v1/__bit_reference:15:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:14:
In file included from ../inst/include/flowWorkspace/wsNode.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/gate.hpp:14:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytolib/include/cytolib/transformation.hpp:697:20: warning: unused variable 'thisMin' [-Wunused-variable]
                        EVENT_DATA_TYPE thisMin=0;//input.min();
                                        ^
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:13: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if(quadPattern == "--")
                        ^~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:425:45: note: uninitialized use occurs here
                CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                        ^~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:417:10: note: remove the 'if' if its condition is always true
                else if(quadPattern == "--")
                     ^~~~~~~~~~~~~~~~~~~~~~~
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:410:5: note: variable 'quad' is declared here
                QUAD quad;
                ^
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:808:12: warning: unused variable 'minRange' [-Wunused-variable]
                                double minRange=atof(transNode.getProperty("minRange").c_str());
                                       ^
In file included from parseFlowJoWorkspace.cpp:10:
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10:
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:
In file included from ../inst/include/flowWorkspace/workspace.hpp:10:
In file included from /usr/local/clang7/include/c++/v1/vector:270:
In file included from /usr/local/clang7/include/c++/v1/__bit_reference:15:
In file included from /usr/local/clang7/include/c++/v1/algorithm:644:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'trans_global' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                         ^
/usr/local/clang7/include/c++/v1/memory:1728:18: note: in instantiation of member function 'std::__1::allocator<trans_global>::destroy' requested here
            {__a.destroy(__p);}
                 ^
/usr/local/clang7/include/c++/v1/memory:1596:14: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::__destroy<trans_global>' requested here
            {__destroy(__has_destroy<allocator_type, _Tp*>(), __a, __p);}
             ^
/usr/local/clang7/include/c++/v1/vector:421:25: note: in instantiation of function template specialization 'std::__1::allocator_traits<std::__1::allocator<trans_global> >::destroy<trans_global>' requested here
        __alloc_traits::destroy(__alloc(), _VSTD::__to_raw_pointer(--__soon_to_be_end));
                        ^
/usr/local/clang7/include/c++/v1/vector:364:29: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::__destruct_at_end' requested here
    void clear() _NOEXCEPT {__destruct_at_end(__begin_);}
                            ^
/usr/local/clang7/include/c++/v1/vector:458:9: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<trans_global, std::__1::allocator<trans_global> >::~__vector_base' requested here
    template <class _Tp, class _Alloc> friend class _LIBCPP_TEMPLATE_VIS vector;
                                                                         ^
/usr/local/clang7/include/c++/v1/memory:1866:64: note: qualify call to silence this warning
    _LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
                                                               ^
5 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib"
ar rs "/Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/lib/libflowWorkspace.a" RcppExports.o parseFlowJoWorkspace.o
ar: creating archive /Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/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 CytoML.so RcppExports.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/GatingSet.pb.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RProtoBufLib/lib/libprotobuf.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib CytoML.so; fi
installing to /Users/biocbuild/bbs-3.10-bioc/meat/CytoML.buildbin-libdir/00LOCK-CytoML/00new/CytoML/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘gating’ from package ‘openCyto’ in package ‘CytoML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "CytoML.buildbin-libdir/CytoML/libs//CytoML.so"