Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 395/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.20.0  (landing page)
Elana J. Fertig
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CoGAPS
git_branch: RELEASE_3_17
git_last_commit: 6861e5b
git_last_commit_date: 2023-07-11 13:53:11 -0400 (Tue, 11 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    ERROR  skippedskipped

INSTALL results for CoGAPS on kjohnson2


To the developers/maintainers of the CoGAPS package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: CoGAPS
Version: 3.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoGAPS
StartedAt: 2023-10-15 18:32:32 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 18:36:56 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 264.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 the compiler supports GNU C++... yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... (cached) yes
checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... (cached) none needed
./configure: line 3246: AX_COMPILER_VENDOR: command not found
./configure: line 3247: AX_COMPILER_VERSION: command not found
./configure: line 3259: AX_OPENMP: command not found
building on  compiler version 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Cogaps.cpp -o Cogaps.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GapsParameters.cpp -o GapsParameters.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GapsResult.cpp -o GapsResult.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GapsRunner.cpp -o GapsRunner.o
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<SparseNormalModel>, Matrix>' requested here
        return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
               ^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, Matrix>' requested here
        return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
               ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<SparseNormalModel>, Matrix>' requested here
    return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
           ^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, Matrix>' requested here
        return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
               ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<DenseNormalModel>, Matrix>' requested here
        return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
               ^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, Matrix>' requested here
    return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<DenseNormalModel>, Matrix>' requested here
    return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
           ^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, Matrix>' requested here
    return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<Matrix>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:113:12: note: in instantiation of function template specialization 'run_helper<Matrix>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<SparseNormalModel>, std::basic_string<char>>' requested here
        return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
               ^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, std::basic_string<char>>' requested here
        return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
               ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<SparseNormalModel>, std::basic_string<char>>' requested here
    return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
           ^
GapsRunner.cpp:85:16: note: in instantiation of function template specialization 'chooseSampler<SparseNormalModel, std::basic_string<char>>' requested here
        return chooseSampler<SparseNormalModel>(data, params, uncertainty, randState);
               ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:70:16: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<AsynchronousGibbsSampler<DenseNormalModel>, std::basic_string<char>>' requested here
        return runCoGAPSAlgorithm< AsynchronousGibbsSampler<DataModel> >(data,
               ^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, std::basic_string<char>>' requested here
    return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
    switch (phase)
            ^~~~~
GapsRunner.cpp:74:12: note: in instantiation of function template specialization 'runCoGAPSAlgorithm<SingleThreadedGibbsSampler<DenseNormalModel>, std::basic_string<char>>' requested here
    return runCoGAPSAlgorithm< SingleThreadedGibbsSampler<DataModel> >(data,
           ^
GapsRunner.cpp:88:12: note: in instantiation of function template specialization 'chooseSampler<DenseNormalModel, std::basic_string<char>>' requested here
    return chooseSampler<DenseNormalModel>(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:104:12: note: in instantiation of function template specialization 'chooseDataModel<std::basic_string<char>>' requested here
    return chooseDataModel(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:119:12: note: in instantiation of function template specialization 'run_helper<std::basic_string<char>>' requested here
    return run_helper(data, params, uncertainty, randState);
           ^
GapsRunner.cpp:430:13: note: add missing switch cases
    switch (phase)
            ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c GapsStatistics.cpp -o GapsStatistics.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c atomic/Atom.cpp -o atomic/Atom.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c math/Math.cpp -o math/Math.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c math/Random.cpp -o math/Random.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)