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This page was generated on 2021-09-13 15:05:56 -0400 (Mon, 13 Sep 2021).

INSTALL results for CoGAPS on nebbiolo1

To the developers/maintainers of the CoGAPS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoGAPS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 360/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.12.0  (landing page)
Elana J. Fertig
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/CoGAPS
git_branch: RELEASE_3_13
git_last_commit: c297d7e
git_last_commit_date: 2021-05-19 11:45:58 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CoGAPS
Version: 3.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CoGAPS
StartedAt: 2021-09-12 06:14:55 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 06:17:16 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 140.8 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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++14 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
./configure: line 2721: AX_COMPILER_VENDOR: command not found
./configure: line 2722: AX_COMPILER_VERSION: command not found
./configure: line 2733: AX_OPENMP: command not found
building on  compiler version 
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  105 |         #pragma omp parallel for num_threads(nThreads)
      | 
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:27:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
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]
  430 |     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++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
   64 |     #pragma omp critical(AtomicInsertOrErase)
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
  101 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:107: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
  107 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:113: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
  113 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:119: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
  119 |     #pragma omp atomic
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
   60 |         #pragma omp atomic
      | 
data_structures/HybridVector.cpp:65: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
   65 |     #pragma omp atomic
      | 
data_structures/HybridVector.cpp:77: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
   77 |         #pragma omp atomic
      | 
data_structures/HybridVector.cpp:82: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
   82 |     #pragma omp atomic
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   26 |     #pragma omp parallel for num_threads(nThreads)
      | 
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Math.cpp -o math/Math.o
In file included from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:12,
                 from /home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10,
                 from math/Math.cpp:4:
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-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 -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)