Multiple platform build/check report for BioC 3.12 - CHECK report for CoGAPS on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CoGAPS_3.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CoGAPS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoGAPS’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 28.9Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
    libs      8.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CoGAPS
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* installing to library ‘/home/biocbuild/bbs-3.12-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
./configure: line 2752: AX_COMPILER_VENDOR: command not found
./configure: line 2753: AX_COMPILER_VERSION: command not found
./configure: line 2764: 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++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:0:
gibbs_sampler/AsynchronousGibbsSampler.h:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 
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-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:107:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:113:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:119:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/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:60:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:65:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
data_structures/HybridVector.cpp:77:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:82:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/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:26:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Math.cpp -o math/Math.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)

Tests output


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoGAPS)
> 
> test_check("CoGAPS")

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on GIST.matrix (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
    worker 2 is starting!
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
    worker 1 is starting!
    worker 2 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 4 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 2 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 4 is starting!
    worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.10.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.12-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
    worker 1 is starting!
    worker 3 is starting!
    worker 2 is starting!
    worker 5 is starting!
    worker 4 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 7 | SKIP 3 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 49.392  10.812  33.156

name	user	system	elapsed
CoGAPS	0.472	0.016	0.505
CogapsParams	0.004	0.000	0.003
GWCoGAPS	0	0	0
binaryA-methods	0.036	0.000	0.036
buildReport	0	0	0
calcZ-methods	0.036	0.000	0.035
checkpointsEnabled	0.000	0.000	0.001
compiledWithOpenMPSupport	0	0	0
getAmplitudeMatrix-methods	0.028	0.004	0.035
getClusteredPatterns-methods	0.032	0.004	0.037
getCorrelationToMeanPattern-methods	0.036	0.000	0.037
getFeatureLoadings-methods	0.032	0.004	0.035
getMeanChiSq-methods	0.036	0.000	0.036
getOriginalParameters-methods	0.028	0.004	0.034
getParam-methods	0.000	0.000	0.001
getPatternMatrix-methods	0.036	0.000	0.036
getRetinaSubset	2.088	0.484	2.951
getSampleFactors-methods	0.032	0.000	0.033
getSubsets-methods	0.024	0.000	0.023
getUnmatchedPatterns-methods	0.028	0.000	0.028
getVersion-methods	0.036	0.000	0.035
patternMarkers-methods	0.088	0.000	0.086
plotResiduals-methods	0.032	0.000	0.034
reconstructGene-methods	0.036	0.000	0.034
scCoGAPS	0	0	0
setAnnotationWeights-methods	0.004	0.000	0.002
setDistributedParams-methods	0.004	0.000	0.002
setFixedPatterns-methods	0.036	0.000	0.036
setParam-methods	0.004	0.000	0.002

CHECK report for CoGAPS on malbec1

Summary

Command output

Installation output

Tests output

Example timings