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BUILD BIN report for CancerInSilico on merida1

This page was generated on 2020-04-15 12:44:21 -0400 (Wed, 15 Apr 2020).

Package 221/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CancerInSilico 2.6.0
Thomas D. Sherman
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CancerInSilico
Branch: RELEASE_3_10
Last Commit: 96c0a6f
Last Changed Date: 2019-10-29 13:10:08 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: CancerInSilico
Version: 2.6.0
Command: rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CancerInSilico.buildbin-libdir
StartedAt: 2020-04-15 07:00:44 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:02:49 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 125.3 seconds
RetCode: 0
Status:  OK 
PackageFile: CancerInSilico_2.6.0.tgz
PackageFileSize: 2.738 MiB

Command output

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###
### Running command:
###
###   rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CancerInSilico.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CancerInSilico.buildbin-libdir CancerInSilico_2.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CancerInSilico’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RunModel.cpp -o RunModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c OffLatticeModel/OffLatticeCellBasedModel.cpp -o OffLatticeModel/OffLatticeCellBasedModel.o
In file included from OffLatticeModel/OffLatticeCellBasedModel.cpp:1:
In file included from OffLatticeModel/OffLatticeCellBasedModel.h:6:
In file included from OffLatticeModel/../Core/CellBasedModel.h:6:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang7/include/c++/v1/unordered_map:384:
In file included from /usr/local/clang7/include/c++/v1/__hash_table:16:
/usr/local/clang7/include/c++/v1/memory:1866:58: warning: destructor called on non-final 'OffLatticeCell' 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<OffLatticeCell>::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<OffLatticeCell> >::__destroy<OffLatticeCell>' 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<OffLatticeCell> >::destroy<OffLatticeCell>' 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<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::__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<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::clear' requested here
        clear();
        ^
/usr/local/clang7/include/c++/v1/iterator:1427:74: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::~__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();}
                                                               ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Core/Cell.cpp -o Core/Cell.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Core/CellType.cpp -o Core/CellType.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Core/Drug.cpp -o Core/Drug.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Core/Random.cpp -o Core/Random.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Tests/Core/test-Drug.cpp -o Tests/Core/test-Drug.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Tests/Core/test-Point.cpp -o Tests/Core/test-Point.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Tests/Core/test-Random.cpp -o Tests/Core/test-Random.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
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 CancerInSilico.so RunModel.o RcppExports.o CellModels/DrasdoHohmeModel.o OffLatticeModel/OffLatticeCell.o OffLatticeModel/OffLatticeCellBasedModel.o OffLatticeModel/OffLatticeRadiusSolver.o Core/Cell.o Core/CellBasedModel.o Core/CellType.o Core/Drug.o Core/Random.o test-runner.o Tests/Core/test-CellType.o Tests/Core/test-Drug.o Tests/Core/test-Point.o Tests/Core/test-Random.o Tests/Core/test-SquareLattice.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/CancerInSilico.buildbin-libdir/00LOCK-CancerInSilico/00new/CancerInSilico/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (CancerInSilico)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.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" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.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" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"