Thomas D. Sherman
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CancerInSilico |
| Branch: master |
| Last Commit: c5b1f65 |
| Last Changed Date: 2019-10-29 13:42:08 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:20 -0500 (Thu, 16 Jan 2020).
| Package 220/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerInSilico 2.7.0 Thomas D. Sherman
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: CancerInSilico |
| Version: 2.7.0 |
| Command: rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.7.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CancerInSilico.buildbin-libdir |
| StartedAt: 2020-01-16 10:34:22 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 10:37:04 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 162.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CancerInSilico_2.7.0.tgz |
| PackageFileSize: 2.959 MiB |
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### Running command:
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### rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.7.0.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_2.7.0.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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /usr/local/clang8/bin/../include/c++/v1/unordered_map:408:
In file included from /usr/local/clang8/bin/../include/c++/v1/__hash_table:16:
/usr/local/clang8/bin/../include/c++/v1/memory:1881:58: warning: destructor called on non-final 'OffLatticeCell' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
_LIBCPP_INLINE_VISIBILITY void destroy(pointer __p) {__p->~_Tp();}
^
/usr/local/clang8/bin/../include/c++/v1/memory:1743:18: note: in instantiation of member function 'std::__1::allocator<OffLatticeCell>::destroy' requested here
{__a.destroy(__p);}
^
/usr/local/clang8/bin/../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/clang8/bin/../include/c++/v1/vector:427:25: 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/clang8/bin/../include/c++/v1/vector:370:29: 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/clang8/bin/../include/c++/v1/vector:464:9: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::clear' requested here
clear();
^
/usr/local/clang8/bin/../include/c++/v1/vector:496:5: note: in instantiation of member function 'std::__1::__vector_base<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::~__vector_base' requested here
vector() _NOEXCEPT_(is_nothrow_default_constructible<allocator_type>::value)
^
OffLatticeModel/OffLatticeCellBasedModel.cpp:26:33: note: in instantiation of member function 'std::__1::vector<OffLatticeCell, std::__1::allocator<OffLatticeCell> >::vector' requested here
std::vector<OffLatticeCell> defaultCells;
^
/usr/local/clang8/bin/../include/c++/v1/memory:1881:64: 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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/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-3.11-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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"