Multiple platform build/check report for BioC 3.9 - CHECK report for CoGAPS on tokay2

Package: CoGAPS

Version: 3.4.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoGAPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CoGAPS_3.4.1.tar.gz

StartedAt: 2019-10-16 02:49:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:03:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 866.7 seconds

RetCode: 0

Status: OK

CheckDir: CoGAPS.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoGAPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CoGAPS_3.4.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CoGAPS.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '3.4.1'
* 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 whether package 'CoGAPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 22.8Mb
  sub-directories of 1Mb or more:
    extdata  19.6Mb
    libs      2.2Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CoGAPS/libs/i386/CoGAPS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CoGAPS/libs/x64/CoGAPS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CoGAPS_3.4.1.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.4.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.4.1.zip && rm CoGAPS_3.4.1.tar.gz CoGAPS_3.4.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 42 24.1M   42 10.1M    0     0  64.2M      0 --:--:-- --:--:-- --:--:-- 67.0M
100 24.1M  100 24.1M    0     0  85.4M      0 --:--:-- --:--:-- --:--:-- 87.4M

install for i386

* installing *source* package 'CoGAPS' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from Cogaps.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:61:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                                                                            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsResult.cpp -o GapsResult.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsResult.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsStatistics.cpp -o GapsStatistics.o
In file included from GapsStatistics.h:5:0,
                 from GapsStatistics.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
atomic/AtomicDomain.cpp:153:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -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
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HashSets.cpp -o data_structures/HashSets.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Matrix.cpp -o data_structures/Matrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Vector.cpp -o data_structures/Vector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/GctParser.cpp -o file_parser/GctParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/FileParser.cpp -o file_parser/FileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
gibbs_sampler/DenseStoragePolicy.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Math.cpp -o math/Math.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/MatrixMath.cpp -o math/MatrixMath.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Random.cpp -o math/Random.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/VectorMath.cpp -o math/VectorMath.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/GctParser.o file_parser/FileParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CoGAPS.buildbin-libdir/00LOCK-CoGAPS/00new/CoGAPS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CoGAPS'
    finding HTML links ... done
    CoGAPS-package                          html  
    CoGAPS                                  html  
    CogapsParams-class                      html  
    CogapsParams                            html  
    CogapsResult-class                      html  
    GIST.data_frame                         html  
    GIST.matrix                             html  
    GIST.result                             html  
    GIST.uncertainty                        html  
    GWCoGAPS                                html  
    binaryA-methods                         html  
    buildReport                             html  
    calcCoGAPSStat-methods                  html  
    calcGeneGSStat-methods                  html  
    calcZ-methods                           html  
    callInternalCoGAPS                      html  
    checkDataMatrix                         html  
    checkInputs                             html  
    checkpointsEnabled                      html  
    computeGeneGSProb-methods               html  
    convertDataToMatrix                     html  
    corcut                                  html  
    corrToMeanPattern                       html  
    createCogapsResult                      html  
    createSets                              html  
    distributedCogaps                       html  
    findConsensusMatrix                     html  
    gapsCat                                 html  
    getClusteredPatterns-methods            html  
    getCorrelationToMeanPattern-methods     html  
    getDimNames                             html  
    getFeatureLoadings-methods              html  
    getGeneNames                            html  
    getMeanChiSq-methods                    html  
    getOriginalParameters-methods           html  
    getParam-methods                        html  
    getRetinaSubset                         html  
    getSampleFactors-methods                html  
    getSampleNames                          html  
    getSubsets-methods                      html  
    getUnmatchedPatterns-methods            html  
    getValueOrRds                           html  
    getVersion-methods                      html  
    initialize-CogapsParams-method          html  
    initialize-CogapsResult-method          html  
    isRdsFile                               html  
    ncolHelper                              html  
    nrowHelper                              html  
    parseExtraParams                        html  
    patternMarkers-methods                  html  
    patternMatch                            html  
    plotPatternMarkers-methods              html  
    finding level-2 HTML links ... done

    plotResiduals-methods                   html  
    reconstructGene-methods                 html  
    sampleUniformly                         html  
    sampleWithAnnotationWeights             html  
    sampleWithExplictSets                   html  
    scCoGAPS                                html  
    setAnnotationWeights-methods            html  
    setDistributedParams-methods            html  
    setFixedPatterns-methods                html  
    setParam-methods                        html  
    startupMessage                          html  
    stitchTogether                          html  
    supported                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from Cogaps.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:61:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type {aka long long unsigned int}' [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                                                                            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsResult.cpp -o GapsResult.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsResult.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsStatistics.cpp -o GapsStatistics.o
In file included from GapsStatistics.h:5:0,
                 from GapsStatistics.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
atomic/AtomicDomain.cpp:153:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -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
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HashSets.cpp -o data_structures/HashSets.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Matrix.cpp -o data_structures/Matrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Vector.cpp -o data_structures/Vector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/GctParser.cpp -o file_parser/GctParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/FileParser.cpp -o file_parser/FileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
gibbs_sampler/DenseStoragePolicy.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Math.cpp -o math/Math.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/MatrixMath.cpp -o math/MatrixMath.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Random.cpp -o math/Random.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/VectorMath.cpp -o math/VectorMath.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/GctParser.o file_parser/FileParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.4.1.zip
* DONE (CoGAPS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CoGAPS' successfully unpacked and MD5 sums checked


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
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...

Loading Data...Done! (00:00:03)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
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...

Loading Data...Done! (00:00:03)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00
== testthat results  ===========================================================
[ OK: 73 | SKIPPED: 1 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 232.04  110.29  343.07


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 9 genes and 1363 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running single-cell CoGAPS on 9 genes and 1363 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples

This is CoGAPS version 3.4.1 
Running Standard CoGAPS on 1363 genes and 9 samples
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
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...

Loading Data...Done! (00:00:02)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00

This is CoGAPS version 3.4.1 
Running genome-wide CoGAPS on 1363 genes and 9 samples with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
singleCell           TRUE 
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...

Loading Data...Done! (00:00:03)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00
== testthat results  ===========================================================
[ OK: 73 | SKIPPED: 1 | WARNINGS: 10 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 149.39  108.07  257.62

name	user	system	elapsed
CoGAPS	3.41	1.34	4.95
CogapsParams	0	0	0
GWCoGAPS	0	0	0
binaryA-methods	0.03	0.00	0.03
buildReport	0	0	0
calcZ-methods	0.05	0.00	0.04
checkpointsEnabled	0	0	0
getClusteredPatterns-methods	0.03	0.00	0.04
getCorrelationToMeanPattern-methods	0.03	0.02	0.04
getFeatureLoadings-methods	0.05	0.01	0.06
getMeanChiSq-methods	0.05	0.00	0.05
getOriginalParameters-methods	0.03	0.02	0.05
getParam-methods	0	0	0
getRetinaSubset	1.26	0.35	2.19
getSampleFactors-methods	0.04	0.01	0.05
getSubsets-methods	0.03	0.00	0.03
getUnmatchedPatterns-methods	0.03	0.00	0.03
getVersion-methods	0.03	0.00	0.03
plotResiduals-methods	0.03	0.02	0.05
reconstructGene-methods	0.02	0.01	0.03
scCoGAPS	0	0	0
setAnnotationWeights-methods	0	0	0
setDistributedParams-methods	0	0	0
setFixedPatterns-methods	0.03	0.01	0.04
setParam-methods	0.01	0.00	0.02

name	user	system	elapsed
CoGAPS	2.41	1.41	4.12
CogapsParams	0	0	0
GWCoGAPS	0	0	0
binaryA-methods	0.04	0.00	0.05
buildReport	0	0	0
calcZ-methods	0.04	0.00	0.03
checkpointsEnabled	0	0	0
getClusteredPatterns-methods	0.01	0.01	0.03
getCorrelationToMeanPattern-methods	0.02	0.02	0.03
getFeatureLoadings-methods	0.04	0.00	0.05
getMeanChiSq-methods	0.05	0.00	0.04
getOriginalParameters-methods	0.03	0.00	0.04
getParam-methods	0	0	0
getRetinaSubset	1.21	0.39	1.59
getSampleFactors-methods	0.03	0.00	0.03
getSubsets-methods	0.03	0.00	0.03
getUnmatchedPatterns-methods	0.03	0.01	0.04
getVersion-methods	0.04	0.00	0.04
plotResiduals-methods	0.03	0.00	0.03
reconstructGene-methods	0.05	0.00	0.05
scCoGAPS	0	0	0
setAnnotationWeights-methods	0	0	0
setDistributedParams-methods	0	0	0
setFixedPatterns-methods	0.03	0.02	0.05
setParam-methods	0	0	0

CHECK report for CoGAPS on tokay2

Summary

Command output

Installation output

Tests output

Example timings