Thomas D. Sherman
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CancerInSilico |
| Branch: RELEASE_3_8 |
| Last Commit: e7cf62c |
| Last Changed Date: 2019-01-04 13:21:03 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:00 -0400 (Tue, 16 Apr 2019).
| Package 197/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CancerInSilico 2.2.1 Thomas D. Sherman
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] | |
| Package: CancerInSilico |
| Version: 2.2.1 |
| Command: rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CancerInSilico.buildbin-libdir |
| StartedAt: 2019-04-16 03:47:29 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:49:47 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 138.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CancerInSilico_2.2.1.tgz |
| PackageFileSize: 3.267 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CancerInSilico.buildbin-libdir && mkdir CancerInSilico.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CancerInSilico_2.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CancerInSilico.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CancerInSilico.buildbin-libdir CancerInSilico_2.2.1.tar.gz'
>>>>>>>
* installing *source* package ‘CancerInSilico’ ...
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RunModel.cpp -o RunModel.o
In file included from RunModel.cpp:4:
In file included from ./CellModels/DrasdoHohmeModel.h:7:
In file included from ./CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7:
In file included from ./CellModels/../OffLatticeModel/../Core/SquareLattice.h:10:
In file included from ./Core/Lattice.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c CellModels/DrasdoHohmeModel.cpp -o CellModels/DrasdoHohmeModel.o
In file included from CellModels/DrasdoHohmeModel.cpp:1:
In file included from CellModels/DrasdoHohmeModel.h:7:
In file included from CellModels/../OffLatticeModel/OffLatticeCellBasedModel.h:7:
In file included from CellModels/../OffLatticeModel/../Core/SquareLattice.h:10:
In file included from CellModels/../OffLatticeModel/../Core/Lattice.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c OffLatticeModel/OffLatticeCell.cpp -o OffLatticeModel/OffLatticeCell.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -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:7:
In file included from OffLatticeModel/../Core/SquareLattice.h:10:
In file included from OffLatticeModel/../Core/Lattice.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c OffLatticeModel/OffLatticeRadiusSolver.cpp -o OffLatticeModel/OffLatticeRadiusSolver.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Cell.cpp -o Core/Cell.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Core/CellBasedModel.cpp -o Core/CellBasedModel.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Core/CellType.cpp -o Core/CellType.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Drug.cpp -o Core/Drug.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Core/Random.cpp -o Core/Random.o
In file included from Core/Random.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
^
<scratch space>:209:2: note: expanded from here
message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-CellType.cpp -o Tests/Core/test-CellType.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Drug.cpp -o Tests/Core/test-Drug.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Point.cpp -o Tests/Core/test-Point.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-Random.cpp -o Tests/Core/test-Random.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
In file included from Tests/Core/test-SquareLattice.cpp:4:
In file included from Tests/Core/../../Core/SquareLattice.h:10:
In file included from Tests/Core/../../Core/Lattice.h:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_map.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_map.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -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-3.8-bioc/meat/CancerInSilico.buildbin-libdir/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
* 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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/Resources/lib/libquadmath.0.dylib" "CancerInSilico.buildbin-libdir/CancerInSilico/libs//CancerInSilico.so"