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INSTALL report for CoGAPS on malbec1

This page was generated on 2020-04-15 12:05:57 -0400 (Wed, 15 Apr 2020).

Package 337/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.6.0
Elana J. Fertig
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CoGAPS
Branch: RELEASE_3_10
Last Commit: 97325f7
Last Changed Date: 2019-10-29 13:08:16 -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: CoGAPS
Version: 3.6.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CoGAPS
StartedAt: 2020-04-14 18:35:34 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:38:03 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 148.7 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CoGAPS
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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... 7.5.0
checking for OpenMP flag of C++ compiler... -fopenmp
building on gnu compiler version 7.5.0
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c GapsRunner.cpp -o GapsRunner.o
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
     switch (phase)
     ^~~~~~
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.10-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-3.10-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/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.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/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -fopenmp -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)