CoGAPS 3.4.1
Elana J. Fertig
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_9 |
| Last Commit: 01d5480 |
| Last Changed Date: 2019-06-26 14:45:46 -0400 (Wed, 26 Jun 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 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 | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CoGAPS
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CoGAPS’ ...
** 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 g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking for C++ compiler vendor... gnu
checking for a sed that does not truncate output... /bin/sed
checking for C++ compiler version... 7.4.0
checking for OpenMP flag of C++ compiler... -fopenmp
building on gnu compiler version 7.4.0
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from include/boost/smart_ptr/shared_ptr.hpp:28:0,
from include/boost/shared_ptr.hpp:17,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from include/boost/shared_ptr.hpp:17:0,
from include/boost/date_time/gregorian/greg_month.hpp:14,
from include/boost/date_time/gregorian/greg_ymd.hpp:16,
from include/boost/date_time/gregorian/greg_calendar.hpp:17,
from include/boost/date_time/gregorian/gregorian_types.hpp:19,
from include/boost/date_time/posix_time/posix_time_config.hpp:18,
from include/boost/date_time/posix_time/posix_time_system.hpp:13,
from include/boost/date_time/posix_time/ptime.hpp:12,
from include/boost/date_time/posix_time/posix_time.hpp:15,
from GapsRunner.cpp:17:
include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp.h:27,
from data_structures/../utils/GapsAssert.h:7,
from data_structures/../utils/Archive.h:4,
from data_structures/Matrix.h:4,
from GapsParameters.h:4,
from GapsStatistics.h:4,
from GapsResult.h:4,
from GapsRunner.h:4,
from GapsRunner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/GctParser.cpp -o file_parser/GctParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/Math.cpp -o math/Math.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/FileParser.o file_parser/GctParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -fopenmp /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/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 (CoGAPS)